I have two very good uses of time travel. Sadly one of them is a major spoiler for the series in question so I can't mention it. I can mention the other, however. Steins;Gate! It's my favorite time travel story of all time, its time travel mechanics are very smartly written. I'm gonna give some minor spoilers on the mechanics in the tag but it's really nothing huge, this is more just a courtesy. (Hold that thought, I actually remembered another really good time travel story that I liked a lot. It uses bootstrap paradoxes and justifies their existence in the world even though they should realistically be impossible and it's actually really good, it's a visual novel called Remember11, check it out)
Anyway as for things that cause plot holes other than time travel, it's making up the plot on the fly, or at least aspects of the plot on the fly. Dragon Ball surprisingly averts this despite being completely made up but it still comes up now and again, Jojo's Bizarre Adventure does this a lot, and even One Piece, despite how tightly plotted it is, creates some plot holes by aspects that weren't initially planned (most notably with haki and certain characters seemingly not knowing about haki despite the fact that they were well should).