It can be easy for player's to stack bonuses (which, is intended lol)! Activating a token that deals damage does not require a roll, correct! And yeah, if a player is attempting to do something outside the "regular" effect of a Token, then calling for an action roll is appropriate. But any immediate effect of the Token only costs the stated Flow.
Also, if you're looking for other ways to tweak the challenge, given how much damage players can output when they're creative/lucky, adjusting the overall stakes of the scene is a good idea! Different time limits, environmental changes (I ran a session where the battlefield shifted to be in the middle of "traffic" and players had to dodge cars and stuff on top of dealing with the enemies), changing the parameters of a mission, all of that sort of stuff is a great GM tool to keep in your pocket. And all of those challenges would fall under "changing the battle in a big way" too!