Perhaps at the start it was mainly cannons and beams going through the shield due to the bug of T2849. That still appears to be working fine, but the remaining hull damage I saw happen was caused by missiles fired from a different sector than the shield group/entity was in.
Seems to happen for all missiles types (although it is expected of the bomb), it's possible the fix for the cannons and beams made it happen for missiles instead or already happened but went unnoticed.