These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Moral Event Horizon: Crocker crosses this when kidnaps and tortures Wanda to use as a source of power.
Arguably, Timmy's parents over all the lies they've been telling him and admitting it all makes things easier for them.
What an Idiot: Timmy did make a dumb move by taking the magical muffin to school instead of just wishing for a magical safe or something to keep the muffin safe in. On the other hand, Wanda said that muffin's magic was too powerful to be affected by fairy magic. So, Timmy's options were pretty limited especially with Crocker spying on his every move. The only other option would be to leave it with his parents who really are idiots.
But it wouldn't matter if the muffin wouldn't be affected by a magical safe, as the muffin itself wouldn't do anything but sit there. Even if that were a problem, Timmy could just get a non-magical plate from the kitchen.