Pain on the 5th Metatarcel and Cuboid I have got a new set of clipless pedals and shoes. Hardly used it for some 15 rides.
Whenever I use it I feel a pain on my left foot's 5th Metatarcel and Cuboid bones.
There is no pain whatsoever on the right foot.
I am using this pedals and this pair of shoes.

On the right set, The shoe is tightly set to the pedals after locking, that is, there is no lateral swivelling of my foot while riding.
But on the left side, my foot slightly swivels laterally. Could this be the reason?

Please let me know, if you had any similar pain and how you controlled it...
With these shoes you probably use Shimano's SPD-pedals or similar MTB pedals. Most, if not all of these do have some angular float of the heel when the clip is engaged. It is part of the system. I'd worry if there's no float.
As with the pain on your left foot it could be caused by the position of the foot on the pedal. Ideally the axle of the pedal would be under the ball of the big toe. You might experiment here by moving the cleat fore or aft. Go for a ride, take along an Allen key and experiment settings.