I'm going to reiterate some of what was already posted...
Why is your kitten having a fecal exam done? As stated, if you're looking at a routine fecal exam, then if parasites are present, it would be likely that all of the kitties would be affected -- especially if they share a litter box or groom one another. Therefore, any stool from the litter box could be collected and used (or, as previously mentioned, the stool could be mixed). However, if your kitty has been exhibiting symptoms that are requiring a fecal exam for diagnosis, it would be best if only that cat's stool is used for the exam.
I'm lucky in that I can tell my cats' stool apart, but not everyone is able to do that. In any event, there are things that you can do. First and foremost, it is possible for your vet to obtain stool for a fecal exam while your kitty is in the office via a fecal loop. It's truly no more invasive than having your cat's temperature taken and is done in less than a minute. Unfortunately, however, if your kitty has recently used the box, stool may not be available to collect. But, in most instances, that isn't a problem. Also, separating your kitty for a couple of hours after a meal or watching when he uses the pan and then scooping up the stool immediately after is also a viable option.
If all else fails, call your vet's office. I'm sure they can always provide additional information to you. Good luck and let us know how it all works out.