Sometimes when I'm trying to fight, I can only attack the first enemy, is that meant to be the cast? Like, if there's Goons A and B next to each other, are you supposed to be able to only attack 'A' until A is down, and then move onto B?
It's most likely your mouse cursor resting over the place where Goon A is, which makes RPG Maker games focus on that since it also has mouse/touch functionality by default. Next time it happens, try moving the mouse to see if you are able to select the other enemies.