You are on to a very important issue that many nonprofits overlook, partly because they never consider that any of their upstanding members would ever sell a raffle ticket and pocket the money, and partly because there is some extra work involved in reconciling the number of tickets distributed with the tickets and money received back.  But failing to make the reconciliation creates exactly the opportunity for skimming that you suggest.  Since none of the purchasers expects to win anything, no one is ever likely to raise the issue.  The organization will never know if it is getting all of the money that people want to give it.

I see no reason why you can’t establish rules by which the participants have to return the tickets and the money before the raffle is held as a part of the obligation for participating in the program.  It may not be entirely fair to establish the rules after the event because some of participants probably just threw the unsold tickets away.  But you can — and should — impose the requirement for future events.