I would say it's probably the saddle height. Before you would have been riding a on flats, and wearing shoes with (potentially) a thickish sole (compared to road/MTB shoes). Now you're using clipless pedals, where there's not a lot between contact and the axle and shoes which probably have a thin (yet stiff) sole. Meaning you're having to straighten your leg more than you have been used to and probably more than you should.
I would say it's probably the saddle height. Before you would have been riding a on flats, and wearing shoes with (potentially) a thickish sole (compared to road/MTB shoes). Now you're using clipless pedals, where there's not a lot between contact and the axle and shoes which probably have a thin (yet stiff) sole. Meaning you're having to straighten your leg more than you have been used to and probably more than you should.
Lower you saddle by 1cm at most