I'm having the same issue. Only one foot though.

Because I had ACL surgery 3 mos ago my ortho will not let me use clipless pedals, nor am I allowed to use toe clips. Speedplay makes a neat platform pedal that clips over the X pedals. With the uninjured leg the foot naturally aligns on the ball of the foot but my injured leg aligns in the middle of the foot.

Is it a strength issue in that leg? My PT doesn't know either. BTW, the bike fits me very well.