I think for me the biggest problem is what we understand about physics and FTL and causality. For FTL to happen, I can’t seem to get around the fact that to an observer a ball is thrown before it actually is thrown. So it’s very difficult for me to do sci-fi…
To get problems, you need to have two FTL ships that are in very different reference frames interact in specific ways. There's plenty of ways to avoid that without sacrificing FTL.
What? That isn’t at all what happens and that fundamental misunderstanding is probably why you have trouble. You cannot, ever, “see” something happen before it happens. An observer “sees” it delayed, just like when you see lightning but hear thunder on a delay. The thunder didn’t happen later when you heard it, and you cannot hear the thunder before lightning. You could, however, fly faster than the thunder and hear it twice, just like if you could fly faster than the light, you could see the lightning twice. In neither case can you see the lightning before happens, or hear the thunder before the lightning.