Happened to me too a few times. Not in Safari though, just any fishing spot. I don't know if I'm right, but I observed that this occurs when you try to fish too soon after finishing the previous battle (e.g. you are fishing, you encounter a Pokemon, you defeat it, and you tap the Super Rod hotkey in a split second after the battle screen disappears or even still while it's visible).
A workaround for this problem is just waiting a second before using the rod again. Keeping this in mind, I didn't have this problem.