You have to completely turn off the trainer while it's not in use to prevent crashes. I use it only when I actually want to duplicate items while I'm in the menu, and I don't use it while trading with NPCs. So far doing these hasn't crashed my game.
Yeah I was actually doing that. One time it crashed because I forgot to turn it off, so I was like, okay. Started it up and 5 minutes in w/o the trainer on again, (second day), it crashed, so I figured that one was the game. Third time, I was playing for roughly 20 mins and built a bunch of stuff, then a crash, I had used the cheat for containers at the home but no scavenging yet. Fourth crash was like the third time, only I turned off the trainer and went to go "to night" and did not make it because when I went to hit scavenge (with the trainer off btw) it crashed, and now I'm here. I always turn the trainer off before going "to night" and I use some of my stock if I need to trade (which, I don't really so I don't go around those places unless I need weapon parts/weapons), or whatever, etc, I'll equip the survivor with food to give to random event people, etc.
But yeah so at this point it actually seems fairly random. I turn it on after inspecting what is in a container/pile of rubble/etc at the home, and if I already have those mats, I just take them instead of "infinitying" them, so it clears up room or lets me know that I have used that cupboard or whatever already.
Edit: Should I be using it when I'm actually INSIDE the menu to get items? If so I guess I've been doing it wrong.