I played an earlier version of Insurgence a few months back and did not have this issue.
Now (1.1.7): I've completed all of the current storyline, but have had to do so without using mega evolution a single time. I've read that you need to press Z or shift to toggle your pokemon's mega stone, yet I have never seen any visual indication of this occurring on screen. I've tried resetting the controls to default, and also a fresh download of Insurgence 1.1.7, but nothing is affecting this.
(Purity mode is off. This is on the Windows version)