When enemy resistances are turned on, enemy filters no longer work, as the resistances are completely different enemies that cannot be filtered. This is most apparent when using defense setups that require blacklisting certain enemy types on certain turrets, such as rocket turrets only targeting spitters.
I know, but there is no other option. Prototypes can't be changed at runtime, and putting all prototypes into the filter isn't a great design either. Sadly, you'll need to disable Resistance and install an additional mod, such as Armored Biters, which has fewer resistances.
