We just got the Hoth expansion, and according to the rules we have been playing by, heroes can only choose to bring 1 ally. However, on one of the Hoth missions where the heroes get echo base troopers at no cost and are split between 2 different start points, the mission briefing reads 'Heroes, echo base troopers, AND any other allies are deployed to the blue points, split as evenly as possible' Does this mean that we have played our previous campaigns wrong? We have been playing that if you get an ally for a mission at no cost, that ally is your 1 ally for the board. Can you bring an additional ally on any board where you recieve an ally at no cost, or just on this one?

Any 'free' allies are independent of other allies so yes you can have multiples.

Pg 5, Rules Reference Guide, Rebel Allies: some missions give heroes control of a specific ally for that mission. These figures do not restrict heroes from choosing to deploy another ally to the mission.

Edit: note the bit I left out. The free allies the mission gives you does not give the Imperial player threat. (Since that's already calculated into the initial deployment). Only the ally you add gives threat.