10 players on offense, Illegal formation

[jTheUmp]

Situation:
I'm the Umpire, in a high school game (FED). Team A comes out to start a series with 10 players. As they break the huddle I count ten, double-take, count again, still have a count of 10.

Just as I signal my count to the wing official, the ball is snapped.

At this point, I know two things:
1) the offense only has 10 players on the field (unless they ran a guy on late, which almost certainly would've been considered illegal substitution).
2) Team A definitely has 4 players in the backfield (QB and three running backs in a wishbone formation, so all 4 backs were in my immediate field of vision as the U.

Should I have thrown a flag for illegal formation? Should I have waited until after the play was over so that I could confer with the wing official on Team A's sideline (to see if they ran a player on late)?