Att around 25 minutes T'Pol says that she is "detecting what appears to be a portal, 22 degrees 'north' of our current position". "North"? There is no "north" in outer space.
When Reed is looking over the cargo, he says it's stem bolts but, in a previous episode titled "The Seventh", the same props are used as "spent injector casings." A form of highly toxic waste which can significantly shorten a person's lifespan.
In one scene when Archer is talking to the prisoner, the prisoner is lying on the top bunk. Archer gets angry at a response and opens the door and grabs him. When he does the prisoner is now sitting on the bottom bunk. He would not have had time to change positions in the few seconds it took Archer to enter the room.
When Phlox is looking at his animal cages, you can see a string or wire attached to one of them, presumably the means by which the cages are shaking.