Short answer: To make them funny!
Longer answer: Tooooo maaaaaake theeeemmmmmm funnnnyyyyyyyy.
In all seriousness, the movies we riff on are bad. Very bad. And usually, they're bad for several reasons, including such boring filmmaking details as pacing, editing, and overall coherence.
Just like back in the Mystery Science Theater days, we sometimes edit our Video On Demand titles for comedic value. That's to help you, the viewer, as well as to make the end result more entertaining — or, at least, watchable.
Likewise, if a movie includes scenes of extreme violence, or something else that we think would otherwise detract from folks' being able to actually enjoy the riffing, we will make edits where appropriate.
But we always try to take care to leave whatever plot there is intact, and to make sure that the RiffTrax content you experience is funny first.