If a person in the current party has a chocobo out it will take up that spot but wont show in the PF. Some people do this to prevent people from automatically joining without sending a tell... but if you sent them a tell and they never responded they either found someone else or they were trolling that last spot. Either way they should have been nice and replied to you!

(they really should fix that and show the chocobos on the extra slots in the pt o.<)