Continuity mistake: When Captain Terrell kneels down and says "What the hell is that?" Chekhov's gloved hand can be seen on the left side, but in the next shot Chekhov is already in the next room.
Continuity mistake: When Kirk is marooned by Khan, Carol asks David to show them the Genesis Cave and he says "we can't just sit here", Kirk puts on his glasses, looks at his watch and replies "yes we can", in the very next shot the glasses are gone as David stands up.
Continuity mistake: When the Enterprise is making a run for the Mutara Nebula, they show a scene in a photon torpedo bay. On the wall the sign says "TORP BAY 4." The problem is that the Enterprise only has 2 photon torpedo bays. Bay 1 (Starboard side) and Bay 2 (Port side). This version of the Enterprise has no aft photon torpedo bays.
Continuity mistake: When Admiral Kirk and party arrive in the transport pod, they dock on the port side docking port in the secondary hull. But the airlock they emerge from is in the docking port for the port side torpedo bay, as signified by the sign in the background saying "TORP BAY 2." You can see the docking port they are supposed to have docked at to emerge from on the side of the torpedo launchers, just above of the secondary hull. The reason for this is because they re-used the stock footage from ST:TMP when Kirk and Scotty docked at the same docking port.
Chosen answer: According to the novelisation of the film the Genesis project was initially designed to be capable of creating an entire solar system. While the focus of the project eventually narrowed down to altering an individual planet, the sub-routines necessary to create a star were still in place and were activated when the device detonated within the nebula.
Tailkinker