Time to put something to bed, in reality basic bodyweight movements should not cause pain.
If there is pain during exercise, bodyweight or otherwise, the movement should be modified or stopped, as failure to stop could result in a client using a compensation movement pattern which in the long term will make the problem worse.
Be mindful that with some clients, their EGO will take over and you will either need to punch them in the face and let them know that progress may be slow, but progress is still progress.
With all this in mind it is also important to ensure that there is symmetry between the left and right sides, (hamstring length, balance, mobility etc).
This is not to do with left or right hand dominance in a sport that demands a skill, it is more like equal movement in basic patterns.
N.B: The biggest issue will be when a client works out unsupervised in the gym using a programme, but fails to notice their own bad movement patterning and still strives to push or pull that extra rep, resulting in an injury.