Actually i dont remember it ever selecting a squadron as ninja. I dont think they need goad since they have no TP bars. So its probably something in your settings.
What is your keybind for Cycle enemies (near to far)? Does it have any potential collisions with other actions? For example if its Tab make sure that no Alt-Tab, no Ctrl-Tab, and no Shift-Tab are assigned to anything else. Collisions are explained in the guide: https://miqobot.com/forum/forums/topic/help-keybinds/
Also check settings under:
System -> Character Configuration -> Control Settings -> Filters tab
Some people altered these settings and blocked Miqo from targeting mobs correctly.
If everything is fine in keybinds then try doing it yourself next time you see this. Click Tab when it happens, does it select a mob?
Also what boss do you fight exactly and are there error messages in the log? I might be of more help if i have more info.