I'm sure some will say that this goes in the help section, but I seem to have the problem under control at least for now. Anyway....

I've come across a couple of weird issues involving one specific Sim and their imaginary friend. The first was that after aging to a teen I would lose certain mouse and keyboard functions when trying to place the doll anywhere on a lot. It seemed like even after placing the doll the game still viewed it as if the doll was still trying to be placed. The first time this happened I was able to get past it by moving the doll around a few times until the problem worked itself out, but the second time I had to save and quit then restart the game. I read about deleting the doll so I tried that and things seemed fine, until I loaded my game the next time.

After loading my save I noticed errors for NRaas Relationship Panel, and noticed my Sim was missing most of the people that should be in the relationship panel. Also her imaginary friend was still listed for some reason, even though she is a young adult now and the imaginary friend hasn't shown up since she became a teen, plus there was no image for it and instead of being blank the space was red. Trying to click the image also caused the problem with my mouse and keyboard again but a reset of the character fixed that. The way I got around this problem was simply by using NRaas Relationship Panel (thank god for NRaas mods!) to remove the imaginary friend from the relationship panel, and after doing that all the other characters she knows appeared again and the errors stopped.

Another thing to note is that there was an entirely new doll in her inventory after I had deleted the original one, which when clicking it showed a different name from her original one. I don't know what I should do with this new doll, I'm worried if I try and delete it more weird things will happen. I'm also worried that her original imaginary friend still exists in some way, and that the problems are all because the game didn't handle the transition from child to teen properly. When using NRaas Relationship Panel to right click the imaginary friend in the relationship panel it shifted to a spot as if the imaginary friend was there, so that's a bit of a concern.

Obviously my Sim's imaginary friend is glitched, but I don't really know how to completely fix it. It seems like every time I find a way around one thing something else pops up. What I really want to know is does anyone know what might have caused this? I've seen people mention imaginary friend glitches but I didn't see anyone mention the problems I had (and potentially could still have).

Place the new doll on the ground if you can and use testingcheatsenabled shift-click to object delete it. Then with MasterController on City Hall or an in-game computer try NRaas > MC > Sim > Advanced > Total Annihilation > Type of Sim > Service, look for the IF Service Sim by either the original name or the new one (or both) and select to get rid of them.

Thanks igazor, helpful as always! I've already deleted the original one, and so far no problems. That just leaves the new one if the game even generated one for the doll, though I did notice the message saying it wanting to come out and play so I'm guessing the game did generate the imaginary friend for the new doll after I deleted the old one.

I'd still love if anyone can tell me what might have caused those problems. The Sim that happened to now has a daughter with an imaginary friend, and it would be nice to know what caused those problems so I can avoid history repeating itself.

All I can think of is that the original IF became corrupt. IFs tend to have underlying sims associated with them for when they are in more than the inert doll state. Merely deleting the doll and not getting rid of the sim is known to cause problems in much the same way as testingcheats shift-clicking to delete a regular sims does -- that only deletes a sim's body, not their data and the game will not react well to that when it tries to order such a sim about.

I never really bonded with the entire IF concept and, like many others, got rid of them long ago and use NRaas Retuner to prevent babies from ever being sent one from long lost Uncle/Auntie Whoever.
http://nraas.wikispaces.com/Imaginary+Friend

I think I'll end up just preventing them completely, because I just had another IF glitch for the daughter of the Sim that originally had the problem. I tried deleting the doll and using MC to actually delete the IF like I did for the mother when she had the problem, but then I was still getting messages from Overwatch about the IF being unroutable. I kept trying to delete the dumb thing, but kept getting the unroutable messages every night during the nightly check. So I'll just stop the stupid things from ever being mailed altogether.

I think before I add even more NRaas mods, I'll try my own XML tuning mod I just made. That link you provided showed exactly what I would look for in the GameplayData.package, so I copied the key called OccultImaginaryFriend_0x5377d6a3925bd9cc and just changed the line kChanceToGetImaginaryDollsOnChildBirth to a 0. I'd use Retuner, but I think I have enough NRaas mods for now.

The thing about Retuner is that it can negate the need for dozens or many more such tuning mods, thus potentially making one's setup more efficient. Though admittedly it does add a bit of overhead to the game as it starts up, right around the time the game clock starts moving forward smoothly. It's a lot of fun to mess around with, though. If one is into that sort of thing.