It's safe to say that for 130 years or so (1530 - 1700) the Mughal Empire was ruling 80 - 90% of what is today India and Pakistan. Ever since the time of Babur rebellions broke out every now and then amongst hindu/muslim rulers where various states formed alliances against the Mughal authority such as Afghan/Maratha/Rajput/Jat/Sikh alliances. It was negotiations which decided the sway, not so much as a muslim/hindu war as it was about who granted more lands for support!
During the time of Babur, a Rajput-Afghan alliance formed under Rana Sangha and Mahmud Lodhi (son of Sikandar Lodhi) along with Hasan Khan Meywat. Babur had denounced all who fought against him as Kafirs and gave the war a religious flavour.
Babur makes a statement with regards to the undisciplined yet brave fighting style of the Afghans after the Battle of Khanua "Swordsmen though some Hindustanis maybe, most of them are unskilled in military move and stand, in soldierly counsel and procedure." -- Medieval India by Satish Chandra (p. 34-35)