I can understand logic behind not deploying character spots. If you set one squad, that squad could use up characters that were part of a different team in a previous round and the computer wouldn't know how to redistribute the other characters.
However, I'd think that fleet and character squads could be separate "categories" - if you fill in fleet, it would still auto-deploy characters, and vice versa. Alas, right now it is working as they have designed it, so is not a bug.
Have a nice day!