If you used the deer and wagon, This is likely what caused your issue
driving the wagon leads to a lot of interaction breaking, particularly the bed's ability to activate sleep - save and reload is the only thing known to reset it if it was a seat on the wagon.
The wagon's lock sorta somewhat overrides/replaces the crate's lock.
If you lock the crate and then set it, contents full, on the wagon, and lock the wagon - the items interaction will, largely, break. - if you instead "lock the crate, place it on the wagon * AND THEN * *unlock* the crate, you will likely have no further issue
you don't need to worry about the crates contents going nuts just because you unlocked the crate, because when you lock the wagon, the contents will get locked again, anyway.
So instead of Crate -> Lock applied -> Wagon -> wagon Lock applied to "Lock applied items" - you'll be crate -> locked applied -> wagon -> crate unlock applied -> wagon lock applied