The chopper takes a bullet to the windscreen, leaving a visible hole. That hole then disappears.
When the bad guys discover Mannix has escaped, sunlight is strongly beaming in through the window, but when Mannix was previously shown emerging from the window, the bushes were so heavy that the window could not even be seen. Furthermore, when the scene cuts to the outdoors, this side of the building is the shaded side.
The fate of Leonard Birx's henchmen is never explained. After Mannix is found to have escaped his cell, Brix and the henchmen search the area around the house for him. Only Brix is shown to have returned to the house and was killed in the explosion. Either the henchmen returned to the house with Brix and were caught in the explosion or they took off after the house exploded.