The Mughal emperors have a mixed lineage after Akbar. Doesn't mean they're not Mughal(did I say that?), but they do have rajput in them.
There's a reason why the earlier emperors like Babur look nothing like his great great great...... grandson.
Picture of the last Mughal(Bahadur Shah II) his wife and kids.
This is what happens when you mix with the local population for generations.