As far as I can determine, the weapon was unloaded and ammo was separate, but both were inside the locked case. That is perfectly legal. He went into the bathroom, loaded the weapon, and began his killing spree.

I think they reported that it was checked in legally unloaded. After claiming it, he went into the restroom and loaded it.

Sorry...just saw the above post!

Ammo does not need to be separate, just not loaded. They do not allow loaded magazines, unless they are in a holder which prevents the rounds from coming out. A box or two of ammo with an unloaded (and racked back!) firearm is definitely allowed.

The procedure to check in a firearm is to go to the regular check in area and ask the person for a checked firearm tag. You fill it out. Depending on the airport, the check in agent may inspect the weapon or you may be sent to TSA for a check and x-ray of the weapon. Once this is done, the firearm luggage is locked with a lock that ONLY the passenger has a key.

The red flag would be the firearm being the only luggage. They might have assumed he had a carry on, and only needed to check the firearm. So, it may NOT have been a red flag.