I think this started after I got a "general bag" from the Rube. Mind you, I don't know what a "general bag" is for (and the icon didn't help :-)
First, I notice that some turmeric I picked up went into the same slot in my inventory as my eggs. The image of the turmeric was behind the eggs.
But it got pretty bad, with things ultimately disappearing. The wonderful Meer was making gasses for me and handing them to me, and they'd either appear over or behind another item or disappear entirely. Ditto for the cherries she gave me, so that I could make other fruits for her.
When I went home to drop things off, I think I saved the eggs, but everything else ended up in a mangle, with many things lost entirely.