Issues like this crop up all the time and most of the time they are resolved before the open. The good news is that they aren't reporting any lost trades or trade busts yet so this isn't as bad as the BATS open at BATS:)
Having said that, they've announced that they will cancel all open orders, that is a huge deal, I can't remember the last time they did that.
To put that into perspective, cancelling all open orders would be the Silicon Valley equivalent of Ebay loosing all bids on their current auctions.
NYSE has always been considered second rate in their IT compared to the NASDAQ and BATS and this won't do much for their reputation.
EDIT meant BATS not FB, thanks!
One other point to keep in mind when throwing around hacking conspiracies. The exchanges aren't running on public networks. You can't DDOS them or hack directly into the matching engines. Though I'm sure you can break in via some other NYSE owned network and make your way to the matching engine somehow.
To hook into the exchange you either go through a blessed intermediary like GS or you plug directly in via colocation. You just can't keep pinging the NYSE on port 80 to bring it down.