I was attempting a run after a while not playing the game so forgot a lot of the objectives in the middle of stages. I got to Sorceress of the Valley and after reaching Cia I immediately went after Manhandla without capturing the Ruins Summit or defeating the Dinolfos and Lizalfos Chieftain. After going underground it came back up after the first Manhandla Stalk I defeated but would not take any damage and I wasn't getting bonuses for having multiple characters attacking him. Is this something anyone else has seen before?

To clarify, I did try to complete those objectives when I realized they were there, but I still had the same issues after doing so

I've had it happen to me a lot as well, and I know it was discussed in the discord but I don't remember what everyone thought the cause was.

As far as I know, and from what I've seen, this is only an NG+ thing, but if you damage Manhandla enough and he goes underground without doing the seed attack on the Allied Base, you can't kill him. Don't know exactly why it happens, though.