After Cobb gets a cup of coffee, he sets the pot down next to the coffee maker. Immediately after, we see Beck get himself some coffee, yet he picks the pot up off the burner of the coffee maker.
At 1:00:33 into the movie when Beck is talking to Martin, right after he says "No change, just the one", there was a cut and splice (notice Beck's jaw position when he finished his line).
When Doc is talking to Justin Jones who is in the shower you can see that Jones is wearing black underwear. They become visible at just before 45 minutes in.
In the scene where the piece of the monster is cut off by the door, the wire that pulls the cut off piece down can be seen.
When Willie falls off the ridge, you see her walking among some large tube worms. Immediately before she says "My God", the worm to her left clearly shows a vertical seam where the left/right pieces of the worm were glued together.
When Beck orders "Seven" to zoom in on her helmet camera, her camera is seen to noticeably widen its lens aperture. This would not only fail to provide a closer look at her target, but it would also allow more ambient light into the the system, further obscuring any fine details.
There is no imaginable scenario that would require multiple portable flame throwers on a sub-sea base.
At 1:30:21 when they are on the surface about to be rescued you can see what looks like buildings in the background.
When Doc is typing out a message just before launching the escape bubbles, the keyboard clicks don't match his hand movements; additionally, there's one last key pressed without a click noise.
During the whole 'Who's the hook?' conversation with everyone in the submersion suits, no one's mouth matches the dialogue.
You can see a crew member, probably the camera assistant, visible in the lower left hand corner of the mirror when Beck and the doctor are talking when the disease first makes its appearance.
Before securing the bottle of vodka in his safe, Beck swaps out the vodka with water believing (correctly) that the crew would attempt to get it. When they do get the bottle they each drink the liquid inside to discover the water. Expecting just alcohol, Beck would have had no reason to sterilize the bottle before refilling it. There would be traces of the biologic chemical even in the water.
One of the characters gets the length of her shift incorrect. The opening narration text states "Day 87 of 90 Day Shift". However, at about 11 minutes, Bow says, "It would be just my luck to finish two months' worth of work two miles under, and have the whole place fall apart with just three days left."