While the exterior shots in the protomatter nebula show the Voyager shuttlecraft to be a Type 6 shuttle, the engineering schematics on the interior displays show a Type 8 shuttle.
When Paris picks up the glass in the "glass and spoon" scene. He picks the glass up with his hand cupped slightly under the rim with his left index finger at the rim. He moves the finger down slightly. However, in the next shot, over his left shoulder, his hand is much further down on the glass than just one second before this.
When Neelix gets ready to leave the mess hall before going to the transporter room, he removes his apron. His comm badge is attached to his greenish coat, not his apron. He does not then put on his coat, but when Neelix appears in Seven of Nine's cargo hold and afterwards on the shuttle (never on a pad waiting to be teleported), his comm badge is clearly visible on his coat, but he did, at some point, change out of his red undershirt.
When Thomas Paris uses the "spoon and glass method" to get the attention of everyone gathered in the mess hall, he holds stemware by its rim. Any type of glass held by its rim can not give off that kind of pure ringing tone.
During the shuttle simulation on the Holodeck, Neelix can be seen holding the canister in his right hand when he is struck by the protomatter. However, when the actual accident occurred he can be seen holding it in his left hand instead. Since this is a recreation of the accident he should be holding it in the same hand he held it in during the actual accident.
When Neelix gets up to leave Sick Bay after the Captain's made him aware of what happened on the shuttle, there is white tape on the bio bed to mark where the actor/actress are supposed to be at.