In Terminator Salvation, Skynet makes an absolutely boneheaded decision involving a young Kyle Reese, creating a plot hole that's a mile wide. Time travel stories can be endlessly fascinating, but they can also be incredibly easy to get horribly wrong. Part of that is due to the difficulty of making sure a film's various trips through time don't result in unresolved paradoxes, or other noticeable logic flaws and continuity errors. The more one messes with the past and future, the more the present must be changed to keep up.
That's not to say that some writers aren't capable of crafting time travel stories that makes sense. It certainly does happen, but even the best usually come complete with a bothersome little unresolved plot point or two. That gets compounded many times over when an entire series of films revolves around time travel, such as the Back to the Future or Terminator franchises. There have been six Terminator films made to date, and the amount of continuity snarls just increases with each entry.
In almost the exact middle of the Terminator franchise is 2009's Terminator Salvation, which is kind of a prequel to the original Terminator movie, and kind of a sequel to 2003's Terminator 3: Rise of the Machines. Salvation is set in the far future from both Terminator and Terminator 3, but also takes place prior to John Connor sending Kyle Reese back through time to protect Sarah Connor in the original. If that sounds like an easy recipe for a plot hole, well, it most definitely is.
Terminator Salvation Plot Hole: Why Not Just Kill Kyle Reese?
The bulk of Terminator Salvation takes place in the far off year of 2018. John Connor (Christian Bale) is about to lead an assault on Skynet's headquarters in San Francisco. Part of the reason this is about to take place is that the human resistance has obtained a list of high profile targets Skynet plans to take out soon, John among them. Number one on this list though is a young Kyle Reese, played by Anton Yelchin. John, fully aware due to the nature of The Terminator's existing stable time loop that Kyle will one day become his father, deduces that Skynet must too now be aware of this fact.
This is in itself a bit of a plot hole, as Skynet seems to have no clue that Kyle Reese has any significance in the original Terminator film, but it's not a big enough issue to derail the film's story. The real problem occurs later, when Skynet successfully manages to kidnap Kyle, who again, is said to be their main target at the time. Instead of doing the obvious thing and killing him though, they hold Kyle prisoner and use him to lure John in, seemingly trying to take out two birds with one stone. The issue is that Skynet is an advanced self-aware AI that is now cognizant of the fact that without Kyle Reese, John Connor as they know him will never exist.
Skynet could've taken the much easier path of killing Kyle on the spot, preventing him from ever meeting Sarah back in 1984, and the two ever conceiving John. This would completely alter the timeline, as John would've never existed to lead the resistance at all, and thus Skynet would presumably not have been on the ropes. Skynet had every opportunity to do this in Terminator Salvation, yet chose to play cat and mouse with John instead. One would think machines capable of taking over the world would be smarter than that.