I just watched that the other day and had the same reaction. I was annoyed that the ending moral was "okay, I can't understand it and it's just mysterious and that's okay," rather than "okay, I don't understand how it works NOW, but clearly there's something to this. I should continue to study it and in the meantime treat it as a valuable source of evidence."

I wasn't that annoyed though, because a few episodes prior Twilight had been totally right about a "curse" not being magic at all, with a "scientific explanation" instead.

Also amused that Twilight has a secret science lab with an MRI machine that she never uses again.

Semi relevant; I posted the following LWish thing in a discussion thread on a forum:

"we here have an enormous amount of extremely strong and general evidence that excludes huge areas of hypothesis space. This is the STRONGLY DOMINANT reason you shouldn't believe certain kinds of things even if someone you trust sincerely tells you to. Things like "physical laws don't have exceptions, no exceptions", "¨there are no irreducibly mental (=supernatural) phenomena", "Due to huge flaws in the way human brains work, billions of people CAN be wrong, and frequently are. You can't even trust your own brain.". We have no reason to believe Equestria and ponykind have similar overriding principles. "

(Please note that this was not written for LW, so therefore I were sloppy and also oversimplifying things due to inferential distance.)

I haven't gotten that far yet, but from what I've heard it would indeed.