The upgrade for the bunker says allows 2 more spots. I am only able to pack up to 5 marines at a time inside the bunker.

Hi Dwrek,

Different terran units occupy a different number of slots.

Marines take 1 slot
SCVs take 1 slot
Marauders take 2 slots
Reapers take 1 slot
Ghosts take 2 slots

Can you check your replay and ensure that a marauder or a ghost was not loaded into the bunker with your marines?

Thanks for your report!