If the Octonauts wikipedia page (http://en.wikipedia.org/wiki/The_Octonauts) is correct, the show's airing was 2 years after the founding (and copyrighting of the octocat) of GitHub
The Wikipedia page also notes that the Octonauts are based on books published in 2006, 2 years before the founding of Github.
While I am not a lawyer, I do not think there is very much similarity between the two. Github's Octocat is half-octopus, half-cat. The Octonauts are 8 nautical animals (including an octopus and a cat).
