Both movies suffer the same problem that many big budget summer science fiction films do: the assumption that once disbelief has been suspended for the larger science fiction devices, it's suspended for smaller oversights as well. These movies feature a number of striking unlikelihoods: black holes, time travel, further time travel, sentient and malevolent machines, etc. All of these are fine; if you pay to see a Terminator movie and can't suspend disbelief about future robots, you're .. wrong. It's the smaller inaccuracies that really tend to break a movie for me. In the case of TS, John Connor expends a huge effort to infiltrate skynet's San Francisco headquarters secretly. He calls for backup from the resistance home base. They dispatch a helicopter, which lands in the very middle of the RnD department completely unmolested. They then just leave!
In the case of Star Trek, the planet Vulcan is destroyed by a mining ship, which extends a gigantic laser gun thing into the atmosphere by a ricketyass chain- yes, a chain. Star Fleet is dispatched from light years away and fails to save the planet. Much later in the film, the laser beam is destroyed, unsurprisingly, because somebody shoots at the EXTREMELY LONG CHAIN and it unsurprisingly breaks. Why didn't planet vulcan think to do this earlier?
Eh.