Did they really called flights "wings" in WC on a regular basis? IIRC, they didn't made this
Actually they did.
But it is easy to explain why in Saga some call it flight (although in reality that would not always be correct either, some would be called "package"):
There are people in the Saga team who know how that works in reality, so the real terms sneak in.
The Wing Commander terminology stays in a lot of parts though, because, you know... it is called WING Commander.
I quote the very first mission briefing of Wing Commander 1:
"You rookies’ll be flying with experienced pilots on your first missions. I want the rookies to fly as wingleaders. You vets keep an eye on the kids out there. Here are the assignments. Maverick, you’re leading Alpha wing. Spirit will fly on your wing. She’s quiet, but she knows the ropes. You’re the wingleader, but if Spirit talks, you be sure and listen. Got it?"
EDIT:
Briefing of mission Tamayo 3 in Wing Commander 3:
"If you and your wing can cut through the fighter cover, we might have a shot at destroying those transports."
so yes, it seems to be normal WC terminology.