In the cave, bats attack you if you run. But if you use the active sonar and send out a 'ping', the bats will stop coming after you. That is because bats use sonar to see, they attack the strange noises snake is making and using the sonar tricks them into thinking you are just another bat.
When you fight The Pain, he'll occasionally perform an attack where a swarm of hornets will attach themselves onto Snake and cause damage. The normal way to get past this is to dive into the water. However, there is a much more beneficial strategy. Before the boss fight, equip as many empty Hornet's Nests as possible. After the hornets attach themselves and disperse, check your inventory again. All of those empty Hornet's Nests will be changed to Hives of Pain Hornets, which revive four bars of stamina.