* The virus is apparently an electricity-based lifeform able to sustain itself indefinitely, yet it is "killed" when [[spoiler: the ship it's in is turned off]], or when [[spoiler: the robot it's controlling is destroyed]].
** Power requirements. Running a "host" without external power is a CastFromHitPoints situation--the virus has a choice between going into hibernation or using itself up to keep the system going.
** Electricity has limits on what it can do. Take out a fuse or a breaker and the current is broken and nothing can happen. When the ship was shut down the currents for the entity to move were basically severed and it couldn't do anything about it.
* Also, why does the virus need us for [[spoiler: spare parts]] if the far superior machine it eventually builds was made without our "help"?
** Obviously, it [[spoiler: cannibalised the organic parts it needed from its other robots]].
** Assimilation perhaps? It's not painted as being the most intelligent of lifeforms. Perhaps it intended to integrate the dangerous potential of the virus known as man to make itself more suited for survival on Earth.
* Why exactly is this movie considered a flop? Granted it's not a masterpiece but it seemed like a pretty good movie.
** A box-office-flop is a movie that performs badly and fails to regain at least its budget, let alone make a profit, regardless of its quality. The movie's not the most godawful in existence, but it's more of a guilty pleasure than good, so it didn't bring in the crowds.
** The cast hated it as well. One considers it her trump-card for "shit movies I've been in" discussions.
* From the arrival of the entity to the tugboat discovering the Russian ship eight days have passed. How did several hundred Russian crew members wind up getting entirely killed off or driven away when the initial assault was small, highly vulnerable robotic insects designed for gathering components?
** There was obviously a rich plethora of weapons on the ship, but the crew didn't just walk around with AK-47s. They were in storage. It's possible that the virus's first act was to arm its gatherers and defend the weapons. And prior to the arrival of the gatherers, the Russians would have had no reason to go get weapons first. All they knew was of some kind of intelligence in the computers. Despite what videogames have done to you and I, the typical response to this problem is not to grab a machinegun and shoot everything that's plugged in.
** Nadya was very vague in recounting the happenings of those eight days. For all we know, it was a matter of hours before the first gatherers were constructed. After all, it was on the ship for mere seconds before it had already cracked the access code for the mainframe computer. The bigger machines could have been under construction when the Russians were still busy with the electrical fires on the bridge.
* The virus wanted to pilot the ship to Lord Howe Island, due to the satellite uplinks the British have there to virtually everywhere in the southern hemisphere. However, early in the movie, Foster reads from a book of noteworthy vessels that the Volkov has three parabolic satellite dishes, so it can maintain simultaneous communication with several spacecraft. It's established that only one of the three dishes is broken. Why wouldn't the virus simply establish contact with another spacecraft, and beam itself to somewhere on land? Surely the Mir wasn't the only thing in space that the Volkov could contact.
* Why did the entity decide to remove Everton's head from his own body and mount it onto the chassis of an under construction droid made from robotic legs and the torso of a Russian crew member? Why didn't it instead modify Everton in a manner similar to what happened to Squeakie?
** Squeakie was a quick assimilation, and I believe that the torso used was actually Woods, not a Russian crew member. Before Everton gets assimilated, he makes a comment about him and Woods "working together for twenty years", and I think that the intelligence took that statement literally. "Oh you've been together? I'll just do that," and made the two of them into a single entity. The robot is an alien intelligence after all.