One of the main reasons I got to thinking about this is due to what happens in the gift shop fight. First off, she seems to jump slightly when Cyclops orders her and Storm to back up so he can blast down the massive steel door separating them from Wolverine.
Next, she not only shows herself to be easily intimated by Toad, but also hesitates and appears uncertain what to do, giving Toad an opportunity to slime her and nearly kill her.
Note: While I understand that Sophie Turner's version of Jean Grey did missions in the 80s and 90s, that happened because of the re-written timeline, caused by an event after the first X-Men film.