Basically, people who inspect your character would get a chance to make a perception check opposed by your disguse check to determine that the kitsune isn't what he appears to be. Spells and abilities like Alter Self give a +10 bonus to your disguise check on this opposed roll.
For example, if a kitsune's disguise skill is +10, he takes a 10 on his disguise check, and he uses his change shape ability it would take a DC 30 perception check for someone to notice that something is off.
Maybe your manerisms were off, or some part of the polymorph effect didn't work properly. Kitsune's eyes often seem a bit odd in their humanoid forms. Either way, I think it is kind of up to the GM to determine what the person who makes the perception check figures out though.