Not by design, but by the assignment of several cavalry regiments to the new Dominion, and several very old and prominent infantry regiments.
Most Muslims in the old Indian Army were concentrated in the cavalry regiments, with infantrymen concentrated in the Baloch (the 10th Baluch, including, later, the Bahawalpur Regiment), and the 5 Punjab regiments (the 1st, the 8th, the 14th, 15th and 16th Punjab), and a few in the Rajput Regiment, as well as the Frontier Force and the Frontier Force Rifles.
The entire Frontier Corps, all 8 formations, went to the new Dominion.
Dogras, Sikhs in and out of the old Punjab Regiment, and in the Sikh Regiment, Jats, Rajputs, Garhwalis, at one time clubbed with the Gorkha, and only much later placed in their own Rifles Regiment, Kumaonis, Biharis, Assamese, all existed in very large numbers in the old Indian Army. That is not counting the Mahars, the MLI and SLI and the Madras Regiment, or the Grenadiers, or newly raised regiments post-1947.
When the Baloch and much of the Punjab Regiment separated out, and the old cavalry regiments also gone - Probyn's, Watson's, Lumsden's, Daly's, the Baloch Horse, Fane's - these were among the 'old' cavalry regiments that went away wholesale.