Inadequate Spawn Conditions:

[ImpulsiveLass]

A multitude of surface mobs do not have checks to ensure they spawn on the surface, they only tend to since the surface loads first on worldgen.

This means any mod that allows passive mobs to spawn in loaded chunks will cause seagulls, seals, bald eagles, crows, snow leopards, tusklins, tigers, sunbirds, etc. to spawn underground.

I.E. the eagle only checks for light level so nearby lava in a cave is a valid spawn position.