I currently finished the temple of Set and started the Temple of Harvest. I am loosely following the cluebook to make sure I don't miss something and I realized that some quest items haven't spawned? I think?

I know im supposed to find a Magical Watering Urn in Set's Temple in one of the teleporter rooms but there's nothing there. And the cat that asks me to avenge her owner in the Temple of Harvest also has no shade or whatever spawned in the room in question. Am I missing something? Was I supposed to press a secret button to summon the urn or something? No item shows up on the map.

Hmm...did you download a particular fan patch for Stone Prophet, perhaps one intended to fix the final cutscene? I had an experience where I downloaded a particular patch and then restarted the game, only to find a game breaking bug where the Temple of Set had been "pre-completed" before I entered (i.e. everything in the temple was as though the maps there had been fully completed at the beginning of the game) leaving unable to continue. The way I handled this one was to start a new game without this fan patch, play through until I had almost completed the game, and then apply the patch to view the closing cutscene. (That cutscene will freeze in an unpatched game.) I alerted the person on the GOG forums who posted a link to the patch (not its creator), and they said they would try to leave a message for the creator. I don't know what happened after that and I haven't replayed Stone Prophet since.

I don't know if this has anything to do with your problem, but that was my experience a few years ago. That's all the help I can offer.

https://youtu.be/yysoH2ArQNs?list=PLpxuazQ7SB4wu_HXJ6LFMrtnoCD9aCSFI&t=245

Here's a time stamped video of one of my favorite Let's Players finding the Magic Watering Urn in the Temple of Set.
Maybe double check it with your game, to make sure you were in the correct location?

I set the time stamp slightly early so that you can see him checking the map.

Aight so turns out... I got all the set totems and used them on every door EXCEPT the one that had the Magic Watering Urn so I couldn't open the door anymore and locked myself out. Thankfully I had ONE save file that I didn't overwrite when I was exploring the Temple of Harvest so I went back, unlocked that door and sacrificed instead the empty room to never being opened and that fixed the issue. Even the cat ghost spawned now. Thanks!

Great! Glad it worked out