Are there two separate Mewtwos? In the first movie and the anime series, Mewtwo's voice clearly indicates that Mewtwo is male. In the 16th movie, Mewtwo appears to be  female. It was then shown that that Mewtwo can mega evolve into Mewtwo Y. From this, is it possible that there are two Mewtwos, where the male is Mewtwo X and the female is Mewtwo Y? I know that in the game, Mewtwo does not have a gender, but this is from the anime's perspective.
I did some research and it appears that there are actually two different Mewtwos, as you suggest. I know this sounds a bit outlandish at first, but it is mentioned and supported in numerous different sources.

From GameFAQs:


  In game: genderless
  Real mewtwo from the first movie: male
  New mewtwo from genesect movie: female, apparently


From Pokemon Database:


  The original Mewtwo, created by team rocket (First Movie &amp; Mewtwo Returns), was a male.
  This is the moody Mewtwo you know best.  
  
  The second Mewtwo appears in Genesect and the Legend Awakened and is female.
  
  There is no real evidence for exactly who created this Mewtwo, but it may have been another team following Giovanni's original plans. It could also have to do with the "multiple parallel universes" mentioned to exist in ORAS.  
  
  If this were to be the case, this Mewtwo would have been created at abut the same time in about the same circumstances, but was born a female and may have never met Ash.


In general, it appears that the movies can sometimes operate within different timelines of the regular anime, so these multiple parallel universe theories can exist separately.

From the Bulbapedia entry for Mewtwo, it states that Mewtwo is genderless, but Bulbapedia refers to the games and not the anime/movies.

You can also watch this video, where a semi-popular YouTuber discusses the gender of Mewtwo (and reaches the same conclusion that there are two Mewtwos).