Some enemies like the acid blob, virus or robot may add curse cards to your deck after a successful near attack. You may want to avoid close combat here - or have a trashcan ready. Other enemies like the skull may steal a card, or the zombie even destroy a slot.
If you have problems with a save file, you should check if it is actually changed when entering a new level - otherwise there might be some write protect issue. You can find me on the Everything C64 discord if you want to share the roguebotsave file with me for inspection.