When the map looks confused is it a problem with thinking or linking? Sometimes it is too early to tell. Live with what you have until you find that thought progresses more easily against the arrow. Then fix it.
There is a temptation to make arrows point both ways. Some ideas are so powerful that they deserve to be peers. More often the pages aren't yet clear ideas or they came to the author in the other order. Expect to feel the speed once this has been corrected.