Reverse loops can definitely be a problem, and I have seen reverse loops inside of reverse loops. Real problems! You'll probably solve this with auto-reversers, but you just have to make very certain that you aren't shorting between the rails. That means, in general, that you need your entire train inside the section that's reversing. There are exceptions, but it is a good rule to work with. It would help if you could publish a picture of your layout plan that some of us could study a bit.
