Some of my favourite humour comes from the dissonance created when maths and dry, scientific language is used to analyse creative license. This is a classic example:
I love trying to introspect humour, attempting to articulate exactly what it is about something which makes it so funny. In this case I think it stems from the fact that the source material was intended to be passively consumed. At first, the presenter defies this intention by deconstructing the physics involved — a form of intense seeing.
This on its own might be moderately amusing, but instead of simply saying “this is not possible”, he actually acknowledges the original intention and assumes that it must be possible (“I saw it on TV, it must be true!”).
I think the humour here comes from the fact that, despite clearly having the skills to debunk the animation, he barely even acknowledges that he has that choice, and instead changes his own understanding of the show to make it fit (e.g. the ponies are made of dark matter).