When malum is not present, all the items associated with malum are remove except for the non-foil cards. I'm assuming this also happens for the farmers, aquaculture and create sets.

The cards also behave strangely with kubejs which isn't really your issue but seems like a sign that something strange is going on.

The holiday set from the base mod also has a similar issue.

Foil cards are not separate items, so I would assume this is the source of the first issue. Foiling is determined via NBT data, and their separate inclusion in places like the creative menu is done by adding an additional version with that NBT data. While I have no experience with KubeJS, my assumption for the strange behavior is maybe due to how the Buddycard items are loaded and managed in an abnormal way. I will have to look into some of this at a later date.