The rules for the Polymorph sub-school indicate:
While these spells make you appear to be the creature, granting you a +10 bonus on Disguise skill checks, they do not grant you all of the abilities and powers of the creature.
Let's assume a human druid wild shapes into a cat. I'm curious if this is trying to say that the druid is essentially disguised as a cat and that anyone interested enough could potentially see through the disguise and realize they are not looking at an actual cat. If this is the case, would the disguise penalties still be incurred for being disguised as a different race and different size category?
Disguised as different race: -2
Disguised as different size category: -10
That would mean that the poor druid would have a -2 on his cat disguise and for most druids would mean it wouldn't be too hard for someone to see they're not looking at a real cat.
This seems wrong and I think it is intended that the disguise bonus is there if you're using the polymorph effect to assume a disguise (A specific cat, for instance) but the rules simply are not that clear.
The only thing that pushes the clarity a little further is the spell Disguise Self which reads:
If you use this spell to create a disguise, you get a +10 bonus on the Disguise check.
However, Disguise Self is an illusion and not a polymorph.
Also the action for Disguise (Skill) states:
Creating a disguise requires 1d3 × 10 minutes of work. Using magic (such as the disguise self spell) reduces this action to the time required to cast the spell or trigger the effect.
So do you have to consciously use the disguise skill or are you always assuming a disguise when you cast a polymorph spell?
edit: Some additional examples
House Fly: Assume there was a Vermin Shape IV which allowed for fine-sized forms. I change into a house fly and attempt to attack someone and miss. IF disguise is relevant the target would immediately get a perception roll to discern that this is no ordinary fly (kind of odd since flies buzz around and bump into people regularly). If they get the hint that this is not an ordinary fly they may draw a weapon and defend, otherwise they may just swat at it with their hand. (Obviously if the attack landed and did a bunch of damage they would be the wiser.)
If you would rule that disguise applies because they could tell (somehow) that this fly is not acting like a normal fly then what about the following?
Human->Elf: A human casts Alter Self to become an elf. Besides risking coming off as a weird elf, what exactly would give away the fact that it isn't actually an elf? Could disguise really apply in this situation?
Best Answer
The Disguise bonus is only relevant if you're making a disguise (and therefore a Disguise check) and using (e.g.) Wild Shape to help with it.
Otherwise, the Disguise bonus is irrelevant and no, does not imply that people can just see through the Wild Shape using Perception against the normal Disguise rules.
Notice that nowhere in the rules for Transmutation (polymorph) does it say you have to roll a Disguise check to have or maintain any of the effects of being shapechanged. The bonus is only mentioned so it can be used in other circumstances that do require a Disguise check.
Thinking about a cat hasn't been helpful as an example, so let's start fresh with a different example and consider a bear.
Case 1: You're Wild Shaping into a bear because you want to bear around a forest. Here, Disguise stuff is irrelevant.
Case 2: You're Wild Shaping into a bear because you want to fool the local goblin tribe that you're their totem bear, Great Paw, and you want to give them an "omen" that will make them move out of the forest. Disguise checks will be necessary here to make you look like Great Paw, and Wild Shape gives you a +10.