Answer:
From my point of view they have five differences:
1- Lifetime lenght, Ottoman Empire ( officially Dawlat-i Aliyye which means just and alone “ Empire / Big State ) has remained more centuries instead of Mughal Empire ( Baburides ).
2- Mughal Empire was just located in one subcontinent/peninsula which is Indian subcontinent but Ottoman Empire located in three different continent; Europe, Asia and Africa.
3- Even all Hindustani languages borrow some words from Turkish - especially Urdu language which Urdu means Army in Turkish - there is no Turkish speaking community after the collapse of Mughal Empire. But in Ottoman Empire case, Turkey’s, Azerbaijan’s and Turkish Republic of North Cyprus’ official language is Turkish and there is many strong and not assimilated linguistic minorities in all Empire’s territory.
4- After the Mughal Empire’s collaps the territory created mainly four states; India, Pakistan, Bengaldesh and Sri Lanka. But on the Ottoman’s territory - after the collapse of course - established 45 different country. So it means that the ethnic and religious diversity of Ottomans were more than Mughals.
5- Even Ottomani Turkish took a strong influence from Arabic and Persian; Turkish was the official language of Ottoman Empire. Instead of this truth, Mughal’s official language was Persian.
I hope my answer helps you to understand.