Disclaimer: This is not meant to be an exhaustive list of said problems, just a couple of things I've noticed that annoyed me the most in terms of gameplay oversites and/or bugs.
First, if you switch campus housing between semesters the game does not add your player to the new "family" for said housing. For my first semester i moved into one of the dorms, which were neat and all but I decided I'd rather live in a frat house type environment for the second semester. So I placed a custom house on one of the lots and moved into it. When I moved out of the dorms it made me take my sim out of the dorm "family" but it never added me to the new houses "family" so when I got to the new house my sim was alone. The game definitely allocated sims to live in the new house, just not as roomates and I couldn't tell who was meant to be there and who was not. Because of this I just locked all the exterior doors for all sims but mine and I quickly figured out which sims were meant to be there and which sims were just wandering around. I eventually unlocked the doors for those specific sims and assigned them their beds and computers (a nice touch btw) but they didn't count as actual roommates as defined by the game. To fix this I decided to not enroll for my sims final semester, move back to his home then enroll for the final semester and move back into campus housing but... this brings me to my next issue.
When moving back into your home after finishing at the university, aside from having to rebuy your house, all the furniture will be gone and the house will be unfurnishable. I'm not sure if that's true for everybody but I know my penthouse in San Myshuno was empty and I couldn't buy it furnished when I moved back in. Super lame. Luckily I have that lot saved so I'll just replace it in the world editor, but if I didn't... There needs to be a way to designate a house/location as your original home when leaving for the university so that when you get back everything is as it should be. Actually, now that I'm thinking about it, it's probably because I didn't check "sell all furniture" when I moved out so that's probably my fault. Still, you shouldn't have to sell your house to go to the university. Especially since the game might put in a townie while you're away. Then you, or at least I would, have to introduce said townie/s to the Grim Reaper in order to vacate the house. Sure I could move them out with manage household but, nah, they'd have to die.
Lastly, and this is more of a personal preference, why can campus housing not have stoves? When I was in college the school had campus apartments and they ALL had stoves. We also had family housing, which were basically small townhomes and condos, all of which also had stoves. There were also grills somewhere near every building. The only housing that didn't have stoves were the dorms, and I guess that's why it's made the way it is buuuut why not just differentiate between dorms and apartments?