User blog comment:Mercrist 089/Scarlet Witch Plothole In Civil War/@comment-3015137-20160518213142

There's some reasons that I've read that were thrown out there. One is that even though she fights fellow Avengers, using mind control is a different type of injury. One can view it as a violation, and while she is currently fighting them, she might not want to cross that line where she uses that power to mentally or emotionally damage her fellow Avengers (not to mention she along with all the Avengers were really pulling there punches in the fight). Another answer I saw was when she used her powers on the ship in AoU, she had the element of stealth on her side and when she used it in Sokovia, she wasn't under threat of battle yet, so it probably requires a level of concentration.