When the shuttlepod leaves to explore the sphere the Enterprise's warp nacelles are lit up. The warp reactor is currently offline due to damage and interference from the spatial anomalies, so the nacelles should be dark like they were in previous scenes.
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.
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 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.
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.
At around 1:20 as a spatial anomaly is sweeping through the corridor and the camera is at ground level a crew member seems to be thrown out of frame to the left. As the crew member is thrown a gray fall mat can be briefly seen.