The Prophet Muhammad(SAW) mentions in a hadith regarding the fitra of a human that an animal gives birth to an animal that is intact, however some animals although rarely, are born deformed in nature and therefore not ‘intact’. Is there a contradiction between this hadith and natural phenomenon, as the Prophet (SAW) must surely have known about deformed animals? Maybe the word “intact’ has a slightly different meaning?
It seems like you are referring to this Hadith:
Allah’s Apostle said, “No child is born except on the fitra and then his parents make him Jewish, Christian or Magian (Zoroastrian), as an animal produces a perfect young animal: do you see any part of its body amputated?” – Bukhari: 441
The Hadith implies that just as an animal is born in its natural intact state the same is true for humans being born with their spiritual disposition – the Fitrah of surrendering to God (i.e. Islam). The analogy continues that just as the animal is blemished by external elements the same is true for humans who lose their sense of Fitrah due to extrinsic influences.
It should be clear from the above that the hadith does not suggest that no animal is born handicap. The hadith is only comparing the state of natural health of a new born animal and the fact that it later may get maimed with the state of a new born human, naturally being with the Fitrah and the fact that he later may deviate from the Fitrah.