Some of them trade for some players, some with op some not oped. But for others it works fine. Spawned in or Naturally gotten items. It's really odd and we can't figure out why it's doing this. We initally thought because of warps or world spawns but that didn't change anything. SOS </3

I have no idea how to help here without information on how to reproduce it. But this is likely not an issue with the Shopkeepers plugin, but either some other plugin interferring, or some inconsistency with the data of the involved items. You can compare item data when the issue occurs via Minecraft's /data command