Ryan says that the hole in Verner's neck came from him falling down the stairs. Falling down stairs doesn't cause puncture marks in the neck.
The mummy clearly isn't in the crate when Ryan opens it to release Micki. It only appears when Micki notices it, after she leaves the crate.
This episode supposedly takes place in an American museum, but when Jack, Micki, and Ryan stage a nighttime break-in, the doors are clearly marked "Royal Ontario Museum".