I hated the missions with Shazam/Hawkgirl/whoever where you had to dodge/hit rocks.
The background have this dark grey stormy thing going on that looks really unpleasant, is incredibly distracting, and actually hurt my eyes because I was concentrating so hard to see my character while looking for specific rocks.
They seriously need to change that background. Also, I have my controller mapped so that Heavy attack and character trait are in different positions. But every time I played one of the missions where you have to protect earth from asteroids it would switch my controls back (pressing B would fire A and vice-versa), which made it confusing for a bit.
The mission were you have to race Superman around the world and the mission where you brainwash Grundy (Red Son) are hard if you want three stars while being frustrating because they're just button mashing. And come on, you know that YOU are the fastest button masher ever, and that you couldn't possibly mash any harder. Right?
Also, as previously mentioned: fuck missions where you have to "Win a clash" or even worse, "get hit by a super move." The computer only seems to beat your ass by stuffing everything you throw out right as you do so. If you just stand there and wait to clash against their attack they mostly stand around, but occasionally throw out interactables or ridiculously simple and low-damage combos, and we all know how difficult it can be to initiate a clash even though we know the input and are inputting it correctly. Personally I get the best luck by just mashing forward plus MB. Don't get me started on "get hit by a super".
A lot of missions are repeated throughout the labs with literally the exact same concepts and star requirements. The arrow shooting minigame and rock-sword-swinging minigames come to mind. These are challenging partially because of their difficulty, but mostly because of boredom thanks to the notion that you've 3-starred this same challenge twice already.
And FINALLY, mission 220, the last Cyborg mission where you have to beat Superman and Wonderwoman back to back while retaining a full second health bar (Basically you get one and they get four), and the mission where you have to fight Killer Frost, Catwoman, Raven and Harley and win with 10% health. I think it was a Hawkgirl mission?
If you read all of this, thanks!