Just a note: I really like the idea of a small amount of very interesting, differently designed creatures instead of adding 1000 random fantasy things. It makes for a completely different challenge and people would treat them more serious.
Yeah, I like making these. The question is how to fit them into the overall lore/atmosphere of the setting. Masterwork seems to be a more-or-less generic fantasy 'verse, so do we really want to go into full 'Our Monsters are Weird' territory?
Some possible 'unusual' creature behaviors:
Small, hard-to-hit creatures that show up in groups and attack relentlessly, but will flee quickly if they start losing (pixies? violent smurfs?)
Deep cavern creatures that can turn your citizens OPPOSED_TO_LIFE if they are encountered. (Something eldritch, probably)
A powerful but normally docile creature that flips out and starts killing everything in sight if it gets so much as a scratch on it.
Monsters that attack at normal speed, but have a speedy teleport-like sprint (blink dogs?)
A powerful pet that might, on rare occasions, go berserk for a few moments, and therefore must be kept chained up far away from your citizens.
A speedy, trapavoid creature that runs away and is almost impossible to catch, but drops a rare item if you manage to kill it (leprechauns?)
A creature that can remove CAN_SPEAK from a target temporarily, which nullifies magic abilities and makes it impossible to give them commands in fort mode.
A creature with a metal shell that can be butchered and melted down for its metal
Cute, fuzzy 1st level cavern creatures that have a caste in every color and can be bred to make multicolored fur clothing.
A plant that infects your citizens and turns them into monsters, which function as useful attack pets (though of course are no longer intelligent). They produce the seed for the infectious plant as eggs, so you can grow them.
...And others.