I have keeper FX and the Nightly patch installed.

Sometimes I cannot pick up creatures with the sidebar, seems to always happen with creatures that I start the game with and sometimes during game but I am not sure what causes it during game.

Sometimes my imps cost 38400 for some random reason.

Is there any way to resolve these?

Yes, the latest nightly build is completely broken. Go back to KeeperFX v0.4.6 r1821 patch, git e229fb3, dated 2016-01-02 23:07:19

I had these problems too. It's pretty annoying that after some of my Imps got killed and creating new Imp cost 38250.

That's no surprise. Anybody who uses the final nightly build will have that problem. Instead, use KeeperFX Unofficial 0.4.6, it's a build with all new fixes/functionality of the nightly builds, but the ones that don't work taken out. Download here.

I've been trying this Unofficial v0.4.6 and have had numerous problems.

Now it's been quite a while since I've played KeeperFX, a few years I think, though I do remember finishing it, while I'm not sure I can finish this Unofficial KeeperFX.

Here's some of the problems I've been having, keeping in mind I don't know if they're limited to the Unofficial or are also present in the normal KeeperFX since it's been so long, I do however not remember having any crashing/graphics problems.

Can't choose to pick up high or low level monsters from the monster panel. (this alone is a serious problem)

Imps often fortify instead of mine gems and sometimes completely ignore gems, keeping in mind fortifying is what they should do when having no other job. (I had to lock them up with the gems at one point)

Can't slap an imp to stop it carrying a body or something.

(Imps all round are a pain, more than usual)

Shift doesn't speed up scrolling, and other minor things I can't remember..

By the time I got to Mirthshire things were going pretty crazy. Mousing over the map would show hundreds upon hundreds of units that aren't there (possibly thousands). https://i.imgbox.com/QlE3Ssuq.jpg

I've noticed the map isn't very good/accurate in this regard, showing things that don't exist and not showing things that do but on Mirthshire it was impossible to remain unnoticed just how bad it can be. Perhaps it had been happening all along, I do know it continued onto the next level as I then kept my eye open for it.

Kept playing Mirthshire and eventually part of the lower screen would flicker black (like blocks vanishing) but managed to finish the level. However the next level, Blaise End, started freezing (not responding) the game.

I was going to say that I'm close to giving up on it, though I just tried two more times while making this post and Blaise End has frozen the game both times after varying amounts of time. Basically I've now given up.

I can't remember what version of KeeperFX I played last time I finished it, I also don't know if one of the later KeeperFX builds work better than this. Though as it stands now it's unfortunately completely blown the wind out of my sails.

The controls on how to pickup creatures from the panel have changed (for a long time now). See this issue. Basically, use Ctrl+click or Ctrl+Shift+Click to pickup highest/lowest level creatures.

Shift still speeds up scrolling, unless in the control configuration you've changed that.

The imp behavior/slapping imps I've made no changes to. Although somebody on Keeperklan also mentioned a problem with mining gems, but I've been unable to reproduce this. Will keep my eyes open for this. If somebody has a saved game on where imps ignore gems, that would be great.

The map issue I've ever seen before.

Now most importantly: There's a bug in the original Dungeon Keeper and KeeperFX that is known as the pathfinding bug. It seems to be more pronounced in KeeperFX as is was in Gold however, and it basically surfaces when there are many possible routes for creatures to take from point A to point B, especially if those possible paths cross separate patches of water/lava. Symptoms are first that units can't find where they want to go, (sometimes this goes as far as dropping an imp next to where it needs to dig and it will just stand there confused), flickering screen until the game finally crashes. The log will then show many 'triangle errors'.
The screenshot you posted has you fortified in, with many tunnelers having many dug tunnels all across the map. This has you more likely to suffer from this bug. My suggestion is to not keep heroes alive forever, and instead kill them quite soon. All the original campaign levels are easy enough that you can kill whatever spawns.