Had pretty much same thing happen to me in an u11s 9v9 match a couple of years ago, one of those did that really just happen moments.
I was standing around the penalty spot, ball slowly rolling out of play. Defender was "seeing it out" under no pressure from an attacker and then picks it up as soon as it hit the line. Immediately thought "that hasn't gone out", looked across at the club assistant who's stood there shaking his head. Blew for the penalty, defender then pipes up "but the ball was out ref", "No it didn't, the whole of the ball must cross the whole of the line", cue mass heads in hands and defender looking like he wanted a hole to open up and swallow him!