this is a fun glitch to run into, and find out hasn't been removed in the definitive edition of hyrule warriors, some thousand hours into my 100% grind. hmm.
what's interesting though is my experience is that its not the dark gohma that's causing the problem, its a wizzro that spawns in wave 3 (this seems to be the majority opinion wrt this issue I've seen online?). and what's interesting about that wizzro, is that as any other character in this mission, the character that spawns here isn't a wizzro, its a ghirahim, which the game turns into a wizzro dynamically if you're playing as ghirahim. The game subtly does this all over the place and its never caused an issue before now. I mean invisible enemies that aren't supposed to be have definitely been a thing but they've all been contained to one level that fixed itself pretty quickly. so idk what's going on exactly or how to fix it, but by god I'm going to try
so, problem was the unloaded/invisible/invulnerable wizzro spawn in wave 3. the spawn was originally a ghirahim that got dynamically turned into a wizzro, so maybe that was the problem. my solution to this: load up in co-op, with player 1 playing ghirahim, and player 2 playing wizzro. the ghirahim spawn can't be ghirahim, because player 1 is ghirahim, so it turns into a wizzro, but it can't be wizzro because player 2 is wizzro, so it turns into a generic darknut. this generic darknut caused no problems and I was able to win. awesome