“This isn’t the first time Twilight showed distrust and paranoia of a “former” bad guy to the point where she doesn’t trust her friends (though given the way Trixie addresses Twilight, it seems she could have backslid as well).”
 
“Apparently, Twilight wasn’t quite as forgiving to Trixie as she believed herself to be. Same goes for Trixie herself considering, you know, Twilight freed her from the influence of the Alicorn Amulet during that last meeting.”
 
“Twilight seems to have forgotten the advice Spike told her at the end of the Crystaling fiasco about letting your students have their space to make decisions for themselves. When she eventually re-learns it, she even tells Starlight this word for word near the end of the episode.”