In "The Tip of The Zoidberg" both the Professor and Mom claim that Zoidberg is an excellent doctor for aliens. But if that is true why didn't he know that Leela wasn't an alien before she found her parents and learned she was a mutant?
Zoidberg is known for:
Having excellent medical knowledge of aliens, considered by Mom
"to be the best in the business, for his price level."
Claims to have little to no experience with human anatomy often appearing to not be able to tell male from female.
Despite this handicap, has manage to perform successful transplants of limbs and even heads on occasion.
Overall, Zoidberg's ability with humans (and thus mutants, such as Leela) to vary significantly in quality and is generally untrustworthy as a resource on the subject, despite his bizarre string of successes from time to time.
There are plenty of planets in the galaxy, and an infinite number in the universe. Zoidberg might have simply not known what species Leela was and been good at treating several alien species, but not humans or Leela's then-unknown species.