Honestly, this is one of the main reasons that the awful "romance" subplot is even more cringe-worthy.

Ignoring the fact that Twilight getting all flustered about this sort of thing feels dreadfully OOC, and that it really has no relevance and does nothing to move the plot forward, (and thankfully, doesn't have any lasting effects…) the creepy part is that she shows considerably less interest in Flash's pony counterpart. In fact, the only reason she blushes at all in the ending is because he reminds her of the human version. The Pony version of Flash actually doesn't seem that interested in Twilight either. He honestly just casually helps her up and walks away.

Anyway, expect waves of fanfiction/art that involve Twilight confiding in Lyra about her new human fetish.