Oh, follow up here for anyone trying to do this as I found the solution, the squadron is bad for Hatali but if you instead check the box “Duty Support” on miqobot and use that system it works wonderfully in Hatali.
The only difference is that rather than trying to command your squadron and going in through that function, duty support has you go in with scion NPC’s, which are much smarter and can easily take down the adds on the final boss before any problems occur.
(you can find Duty Support in your duty menu, youll need to drag it to your hotbar for miqo to work with it)
So a recap; do NOT use your squadron for Hatali, theyre just bad. Use the duty support option.