@Playalot That might work, but I just restarted my game and as soon as I logged in I noticed my some of my plants where in my household inventory again. I'm beginning to think it has less to do with the placement of items and more to do with some glitch. I'm considering uninstalling all my mods and seeing if that works. I know mods can produce weird glitches. I'll let you guys know if that works.
Yea the first thing to do in figuring out what is causing problems is ALWAYS to uninstall all mods and CC from the game to see if that is what is affecting it. Mods are subject to bugs also and sometimes game bug that dont affect a sim directly can crop up when scripts are modified by custom content and start reacting in strange ways. Even with Deaderpool's MC Command Center and him being VERY fast on updating the mod when patches come out, I still uninstall everything custom first to see if the problem occurs with base game files. That way you can say you KNOW with a high degree of certainty it's a game bug and not someones custom mods/files interacting in some strange way with the game.