Three of my pets, Ferngulli, Nanoq, and Dustfinger, have one less intelligence point than books read... I don't understand how that could be. If there is anything that makes a pet lose intelligence I am unaware of it.

All three of these pets are some of my older pets, but I don't know if that has anything to do with it.

When you go to the points shop on the mystic spindles game, it says "Note: If your pet's intelligence is lower than their book count (due to a glitch a while back), raising that pet's intelligence using this shop will fix that problem. If your pet's intelligence is higher than their book count, don't worry, this page will only add intelligence."

So...since you said those pets were older, I'm guessing they got hit by that glitch. One of my older pets has the same problem, too. I don't know if there's any way to fix it other than playing a billion games of Mystic Spindles.

[edit] Oh derp, intel boosters would also fix it. Like Shinwas Key or one of the slimes you can get from the zapper.

Sweeeet, thank you!