i can confirm, it's the bot who cant find a spot to stand, so he skips that fish pool.
what waterwalking does, i dont know exactly, on shaman (with buff set to autocast every 5min (it has a runtime of 10min) i did not see change in behaviour of the bot.It alwys searchs a dry spot to land. (i'm using flying).
sometimes he finds a pool and places himself in a position, where there are plants or others blocking him from fishing.
as i used the bot to get draenor fishing, i just learned to set profiles, where this problems do not occure. So if you know how the bot works, you can avoid specific spots. It's a bit work, but i found out, that done properly the bot works as i want it to.