Most of us have some sort of left or right asymmetry where one side or the other will be more flexible or stronger. There may well be something about your bike fit that is causing your discomfort but it is just as likely the problem is related to your personal asymmetry not something induced by bike fit. I find stretching helpful after a hard ride. Perhaps stretching would help you too.
I find myself pedaling squares when my legs get tired and need to pay attention to remaining loose and relaxed. In the video, although it is about road riding, what strikes me most about it is the cyclist remains relaxed. I'm an old man and asthmatic besides so I need to pay attention to pedaling technique and remaining relaxed everywhere else so that what effort I'm able to put out is directed solely to moving the bike forward.
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