They are about this by way of negative example. In Feeling Pinkie Keen, for example, Twilight Sparkle pulls a Straw Vulcan by refusing to accept some very very strong evidence of things... and, instead of the writers colluding with her, she gets called on it by her friends (this not a spoiler - it happens essentially right away).

Other episodes prominently featuring errors of deduction (that get pointed out, not just plot holes/idiot ball): Bridle Gossip, Lesson Zero, and Griffon the Brush-Off.

Also, in Fall Weather Friends, Twilight Sparkle performs much better in a race than one would expect for a novice because she read up on how to do it well.

I'd agree with Raemon's comment, especially the last two sentences - it's not the best possible show about ponies who are friends, but it's good enough to demonstrate the upper bound on the quality of such shows is much higher than generally suspected.