I had the same problem appear sporadically, but i was able to fish and catch two fishes despite this appearing from time to time. I think that it has to do with distance from water, i think you need to be closer to deep water for it to not happen, although i havent tested it. Basically i think is what happens is when the wave rolls very far back the distance to deep water becomes too little to allow fishing, so fishing cancels.

Can confirm what rowiyo said. You can see that the shallow water has to do with this issue when the waves go back (see clip). If you aim at deeper water where the waves won't expose the land underneath you can fish.

I had the same problem filling the watersack, if you try to do it without getting your feet wet it will work intermittently, i guess you need to go into the water for it to work solidly, but i didnt try it. In that case i dont think that its a bug but rather a game mechanic.