It recently happened to me. I don't know if it's random or not, so the best advice I can give is keep at it.

They usually seem to happen during the MK 1-9 towers, though it wouldn't shock me if there were other towers with secret fights. Also, try ending your fights with brutalities. I've gotten a bunch of the secret fights, and that seems to be one of the common threads I can think of.

I do believe it is entirely based on the tower. Someone posted a way of doing this on a YouTube that I tried and it proved to be 100% false. I do know all the hidden fights I obtained and some more than once.

1. Reptile = you fight him in the MK1 Living Tower, both times I went through the tower it was at the 2nd or 3rd to last fight he'd appear

2. Kitana = you fight her in the MKII Living Tower even is she is on the tower as a normal fight, but the hidden fighter version will always be in the Mourning stance ( paying tribute to Jade )

3. Cyber Sub-Zero = You encounter him in Triborg's Living Tower usually right before the very last fighter

4. Goro & Reptile = in the normal Klassic Tower sometimes, not always, Goro or Reptile appear randomly as hidden fighters. They don't always appear either and the supposed way to find them does not work

I've heard there are other hidden fighters but I haven't seen any except during Invasion Battles the assassin of the realm invading you at the time will randomly pop in a so-called hidden fighter but it is called an Assassin Battle

I'm still wandering if there is one on The Pit?