At 06:20 Stephen pulls the hood off Garibaldi and the scene shifts to Garibaldi speaking. When the scene goes back to Stephen at 06:31, Garibaldi is wearing the hood again until scene change, where he's not again.
During the fight in the tunnel Garibaldi and Franklin knock out the two patrolling guard by punching them. In the next scene when Franklin is stitching up Garibaldi's wound Garibaldi asks Lyta "Hey, you hid the bodies?". It would be very out of character for them to have killed two men in cold blood this way.