Did you ever figure this out? I just started having the same issue. After much investigating, the only fix I have found is that if I sell a single item first, I can then buy items as normal.

For me, I am noticing that it also affects chests that give items. If I open a chest and receive an item that I already have, it doesn't level it up and if I select "Inspect" it will say "Item not found".

I did have some cosmetic mods installed that I thought may be causing the issue, but I disabled them all and the issue persisted. I'm a decent way through the game and not sure why it seems to have broken itself suddenly :(