A lot of places that actually have a hall competition that isn't just a popularity contest based on photos strictly forbid you to enter the same costume in both. Probably precisely to prevent things like accusations that it's not fair. But if this particular con changed the rule to allow that? Gotta be a reason, even if it's a dumb reason like "the con chair said so."
I'm not going to say that it's perfectly cool. I do personally think it's tacky. And a competition that opens up or abolishes rules which keep unfair, gauche, or unethical things from crossing the line and leading to lots of drama and whining is just asking for it. If a lot of people are upset by it, they should voice their opinion to the cosplay staff. But in the end, the staff has the say-so to make and break the rules as they see fit. If you don't like their reasons or think they made/unmade the rules to serve themselves or some weird philosophy of cosplay that doesn't match up with reality, well, the only thing you can do after speaking out is walk away. Don't patronize the contest and encourage your friends to stay away from it as well.
Founder and Vice-President, Madison Area Costuming Society, a chapter of the International Costumer's Guild
Strange Land Costuming - www.strangelandcostumes.com