Proper way : I've seen that before. I delaminated the area, then relaminated it with the Zodiac 7098 Transprene 113M adhesive and clamped it with a welding clamp...that made the bump lay flat and solved the leak.
Less proper way, but still semi-pro way : Latex internal sealant would probably take care of it.
Super-easy, permanent, kinda improper way : If you don't mind a non-professional $10 solution, go buy some Aquaseal + Cotol-240 from your local dive shop. Mix it 50/50 to super-thin it out, then squirt it in to the bump with a syringe while the boat is deflated. It is an adhesive/sealant. I use it a lot for trashed hypalon boats...where the layers are delaminating or the neoprene backer is absent. It's good stuff, but VERY hard to remove if you mess up.
Gluing geek since 2007