Some of your stuff is custom content.(Desk?) Which are sometimes not a desk at all, but something else textured to look and or behave like a desk but one end may be invisible which you may see Sims try to put something on the other end (invisible) and it's taking up two tiles because it's possible it is custom content. I'm almost positive you have something in your downloads causing this if you have any object cc. It also looks like you have the cheat turned on to set things off the grid (not that particular cheat) but another which lets you set things like a quarter over etc. instead of exactly on the grid mark for normal play. The other cheat I speak of is found under Help. All objects need a space to be able to reach them, sometimes some things need two spaces in front of them to space things so Sims can use them. I see you used MOO to make a point, however, I'm almost sure this is caused by cc (something in downloads) and or an activated cheat.
ETA: If the chair doesn't fit in front of a desk then it's a cheat or bad cc in your downloads which is messing up either desks and or chairs. I don't recall that desk in the game, so is that cc? ETA: Did you use cheat to put that ball mit on an angle, perhaps it's your cheats and you need to stop using them if you don't expect some weird occurances. Just sayin' :) Or have you forgotten to turn them off such as 45degreeangle cheat? You know that makes other stuff even if not turned at an angle to mess up, too. You have to use this sparingly. ETA: I don't know what original complaint there was only the pics you have provided and it now is clear it's cheat problems on those lots in the pics I can see. Don't leave them on and and yes they will mess up the game. I run into this when I'm not paying attention to how many spaces things need and what direction and or if other things (like an overhead light or side wall light is blocking) Best advice turn off cheats when building and decorating it's clear the cheats caused all these problems.
ETA: Finally got to see first pic. What did you place there in front of the cc craft table? It's at an angle, you used a cheat no doubt. Move out and back in and redecorate without cheats next time. stop using moo, and 45degreangle cheats and or grid cheats until it's understood and close attention to what is done, and where it's placed. Sims need one or two spaces infront of almost everything (most things ) to use them or get around them. Two spaces at front doors to get into house, one will make them scream they can't get in, two or more at top of stairs, or they will scream they can't go up them, two or more in front of most indoor doors, and one or more in front of paintings etc. to view, and the first picture clearly shows something there that is blocking that craft table (cc) and maybe it's the problem if you don't remember what else you placed on the wall and or near there or whatever while cheats were on. ETA: Oh, it's the bear, sorry for the long lecture but you are causing these problems yourself. The normal vanilla game doesn't behave this way. Sims will set things at an angle sometimes, that's why you can't place things in such small corners and pick it up and move it. However, if it's still at angle then turn off cheats. Too much stuff in a room that doesn't give them enough space to use things is also part of the problem.
Where you placed the potty seat with moo won't work because you should put it in a spot where the parent can move to the semi side and stand to wait for the child to learn or use it. It should have more space around it than that. The commode and potty seats in TS2 can not be used when direclty next to a wall (side) and or not enough space in front of them (potty) for the parent to stand or the toddler to turn around and sit down. This game needs more spaces than TS4. Because it was built so Sims would not clip into objects. Objects Sims may set down at an angle, the bear, toddler toys, or toys etc. It's a common thing ,however, in my experience picking up the bear and moving it to a normal space will cause it to go back to normal but cheats have too be off. ETA: Pets will cause their bowl to turn at an angle, you have to learn to turn it back to a straight position or move it. It's a thing in TS2, yes, and sometimes annoying, but the collision markers are not removed in TS2 like they were in TS4, it's why Sims won't walk through objects (sometimes cc they will) or use them because there are those blockers to make them not collide. But yes a child will put the toys and bear at angles and why when you play, cheats need to remain off. Such as moo, grid cheats and angle cheats so you can pick it up and put it back then turn off.
ETA: One last thing, I promise, lol, sorry not trying to lecture you. If you save a lot with an activated cheat still on did you know you can still use that cheat (though cheats won't be on) when you place it again? Like the 45degreeangle cheat. It would still be activated and could still place chairs etc. at an angle perhaps that is also part of anyone's problem when they don't know why things are going at an angle (maybe they forgot they saved and put in bin while on). But the bear placed by a child at an angle should go back to normal when you have all cheats off and it's cliping into that cc craft table, so yeah, some of the issues may also be collision markers removed from some cc when cheats are on, too.