Continuity mistake: When Reed instructs Archer how to disarm the second arming mechanism of the mine, he tells him to turn the first component clockwise, but then Archer is shown turning it counter-clockwise. Then Reed tells him to turn the rest of the components counter-clockwise, but afterwards he must reverse the last component to keep the mine from rearming, which means turning it clockwise. But when Archer reverses the last component, he turns it counter-clockwise.
Continuity mistake: In the scene in T'Pol's quarters, after she and Tolaris have mind melded and she asked him to leave, he walks out, and the door starts to close before the shot changes to T'Pol. But when the shot changes, the light from the door on T'Pol shows the door still opening, and then closing. (00:33:40)
Continuity mistake: At 38:20, T'Pol (as acting captain) says that they have resumed their course to Azati Prime; however, from 39-42 minutes, Captain Archer and Trip discuss the "current" status - that they are still orbiting the planet and then the Captain orders Trip to tell Travis to set a course for Azati Prime at maximum warp. (00:38:20)
Continuity mistake: The captain's log date of Jan. 8, 2154, doesn't align with the timeline of previous episodes. Harbinger, two episodes earlier, was said to take place Dec. 27. The episode in between that and Hatchery, Doctor's Orders, wasn't given an on screen date, but T'Pol compared the anomaly in that episode to the one in Harbinger, which she said was encountered a few weeks earlier. Even if that was just two weeks earlier, that would put Doctor's Orders at Jan. 10, and that episode spanned at least four days, so the earliest Hatchery could take place would be Jan. 15.
Continuity mistake: When Hayes takes off his jacket before sparring with Reed, he tosses it to his right so that it's on the right side of the room. When he picks it up, it's now against the wall that's on the left side of the room.
Continuity mistake: When Captain Archer is talking to Hoshi in her quarters, at one point he leans against the door-frame. In the next shot of him from that angle, he's no longer leaning, even though we saw him from behind and he didn't move. In the next shot, he's back to leaning against the door-frame.
Continuity mistake: Archer, T'Pol and Trip enter the cloaked Suliban ship, after Trip uses the stun grenade. Archer exits the docking bay first, followed by T'Pol and finally Trip, however in the next shot Archer and Trip are together and T'Pol exits for a second time. Also as she exits the door closes behind her, but in the following shot the door closes again. (00:28:00)