Afore Note : Game version was 1.02 as I played my entire first walkthrough when game was released, I only finished it today, due to exploring every single '?' and every random encounter. I also discovered every single one of these mentioned bugs myself, and has verified they do exist.

System Specs : Windows 8.1 64 bit
GTX 970 driver 350.12 until recently, I updated to 353.06
i7 4790k
16GB RAM

Velen & Novigrad :

>climbing disabled bug
>meirsdorf quest , the apiarian contract cannot open basement bug
>novigrad sewers eye of nehaleni cannot open invisible wall bug
>graphical disturbances with priests of eternal fire, their LODs are contorted with purple texture

Skellige Isles :

>if helped Hjalmar before funeral of King Bran AND you escorted him to the Ice Giant's cave then you return to complete the Master Armorer quest in Velen, when you fight the Archgriffin you will enter the Ice Giant's cutscene and game will freeze and crash
>if helped Hjalmar and not finish his quest and return to Velen or Novigrad you will somehow lose access to AXII sign, sit on a boat and it will reset
>graphical black spots on alot of mountains, and certain areas there are no water texture, completely transparent waterbox and an empty space, locations I've found personally are the islands from south west of Undvik, the small island north of the guarded treasure, treasure guardian is a cyclops

Combat and Animation related :

>monster corpses always lies horizontally and if you kill them on a slope sometimes they float in mid air, it looks awkward
>snow hares corpses cannot be looted for they drop deep underneath the floors
>hens corpses cannot be looted for they drop deep underneath the floors
>roach often dives his head into the side of the mountain when you ride him and climb a steep slope, it looks awkward
>alot of invisible walls are in this game, if possible they should be removed, the majority of them I've encountered are in Skellige, the roads that has wooden plank strips on them blocks roach from moving forward without a jump or leap, locations of these are easily found but for example, a few is located near Fornhala, Holmstein's port, there is also a major invisible wall located at Kaer Trolde castle, I've managed to climb atop the mountain with the tree stomp and axe by going around the castle's outer courtyard
>AXII sign cannot be upgraded with 2 different abilities, one of them will not work, for example having delusion and puppet will disable one of them
>small or low stone walls around Kaer Trolde [and many other locations on Skellige] are also troublesome for roach for he cannot jump over them, their threshold is simply too high for roach to jump across
>when roach is "parked" or is in a barn eating and you whistle he does not forward or comply
>when using a boat/dinghy if you abruptly enter combat immediately after you unuse the [E] function sometimes geralt gets droped from mid air, and many times I've died because of this when I abrupt stop my boat to fight the annoying ekhidnas
>ships with trap doors and other compartments can permanently destroy your progress, a brigantine off the Pirate Coast in Velen did such for me, I had to restore to a save before entering the hidden compartment for underneath was water and from the surface of water I could not climb back out, please seal or block these hidden compartments if they aren't being used
>large abandoned 'ghost ships' that are floating [brigantine model only] cannot be climbed and when trying to do so from a boat/dinghy will result in geralt being dropped from above water continuesly, the animation never stops
>large abandoned 'ghost ships' that are floating [longboat model with ekhidna nests only] cannot be explored when trying to do so will result in geralt being dropped from high above and meet certain death
>the keep or castle on Kaer Gelen has no physical roof and no support for its second floor roof as well as top floor, when climbing atop it will result in geralt being droped deep down into underneath the castle with invisible textures and progress will be terminated
>certain 'wandering' merchants in Skellige changes their mesh/texture when you enter a conversation with them and you cannot engage in trading with these merchants
>the 'Nowhere Inn' has no Innkeeper icon on the map, it makes it difficult to locate it until I became really familiar with Novigrad

Quest Items and Quest related :

>current consensus is that too many quest items stay in the quest category, either make arrangements so quest items can be removed or allow them to be removed via in-game merchant who can buy them
>quest bugs I've personally found are as follows :
>apiarian phantom cannot open basement if you explored the unfinished building before starting quest or accepting the contract
>after you've completed the quest [Carnal Sins] you still see tons of concerned citizen sermons all over Novigrad if you accidentally picked them up they stay in your quest inventory for good
>during [Payback] quest as you accompany ciri to steal the horses afterwards the horses will stay in game permanently, the 3 horses from the barn will wander outside and stay there along with the guard who you've knocked out, he will be in that area everytime you enter it
>during [Spooked Mare] quest if you've used AXII sign to convince the Scoia'tael bandit leader to give one mare, no horse will follow you, and you will have to steal a horse and kill all the bandits in order to complete the quest, this is a bug nevertheless
>after you've completed [Count Reuven's Treasure] quest you will have a random encounter when heading up Electors' Square, this encounter is bugged and when you choose to help the 2 Beggars by killing the Witch Hunters all of the npc and enemies disappear and you end up fighting he city guards and other guards somehow
>one of the druids near Gedyneith who has a quest giver icon on him gives no quest dialogue
>after the main questline progresses past ACT I, there appears to be a merchant icon south of Gedyneith [in the foggy destroyed forest] however no merchant is there
>if you completed the quest [Iron Maiden] and you accidentally pick up the Hornwall Sword after completion of quest you will be stuck with it, tons of quest related items bogged the quest inventory for me this was just one example

items that I've found myself stuck with :
ALOT of keys :
Cage Key, Aged Key, Bandit's Key, Key to Whoreson Junior's Estate x19, Key to Vigi's cage, Key to Prison, [another separate] Cage Key

The decoction of grasses [from Kaer Morhen]
bull figurine
serpent figurine
arrest warrants x3
concerned citizen sermon [Carnal Sins]
eyes from [Redania's most wanted]
Morkvarg's journal
Lever
Phylactery
Squirrel Tail
Wolf Mask
Forktail Spinal Fluid
Letter to Caleb Menge
The Baron's Notes
Distiller's Letter
Distiller's Log
Bomb lid
Bomb part
Script [from Priscilla's play]
Letter to Lighthouse Keeper
Unsent Letter
Berengar's Notes
Monstrum, or a portrayal of Witchers: Volume 2
Mysterious Letter
Mysterious Notes
Letter about treasure [from Fritz]
Short Letter [from Louis to Janne]
Hornwall Horn [from Undvik Hjalmar quest]
Shackles x2 [from Undvik Hjalmar quest]

; and alot of letters and records, all of above were kept after quests were completed

Other Mechanic related problems :

here are my own opinions, others can object to this but I find these problems impact negatively on my gameplay experience and emersion

1. carrying weight, as usual, the carrying weight suffers from the same plague that bothered people since Witcher 2, I loved exploration for this game and somehow it punishes me and others who goes on adventures, the body armors alone in Witcher 3 weights some 20~22kg, it is illogical, chainmails don't weight 22kg, full plates with helm weight that much in real life.
2. money from vendors are too low/insufficient, I often had to travel to upwards of 5+ vendors to sell off all the goods I've hauled from around Skellige, as you level higher even common items sells of upwards of 70 coins each making money easily made and even more pointless
3. money has no real purpose, for me at least, I found that witcher armor was the best and the other craftable equipment are inferior generally, and there is a lack of 'relic' grade armors that are craftable in Witcher 3, so all the money and gems such as [flawless] and other expensive items are useless, it makes money obsolete
4. bolts somehow can't be sold in weapon or armor merchants, they weigh in at about 10kg per 40 shots, they simply weigh too much for them to be practical and I have to destroy them everytime I get some
5. everytime when you fast travel or load a save you lose 10% of power for each of the mutagens, you have to re-apply them in order for them to supply the full 40% of power they are suppose to give [example : Greater Blue Mutagen or Greater Red Mutagen]
6. there appears to be 2 types of runes of each [lesser] and [greater] variety, only the 2% can be used to craft greater while the 5% and 3% cannot, this makes crafting runes obsolete and useless
7. you cannot run while standing on boats, and you cannot cast signs such as quen until after you've entered combat while standing on a boat, it is troublesome for a player may want to cast quen before diving down to prevent annoying drowners from harassment
8. there is no way to organize your inventory [again...] just like Witcher 2, all inventory items are organized by timestamps and I cant permanently organize them myself or view them from a different variable
9. overall Skellige feels not as refined as Velen and Novigrad, it feels less polished, it has less random encounter and random quests overall and more bugs, lack of monster nests, abandoned locations and monster variety