Then in retrospect I feel like a fool having called time out when I saw our Jr. Pee-Wees (less than 12 YO) in an illegal formation.

I guess it depends which league we're talking about. The largest youth league our association covers wants all formation and numbering rules enforced. Now obviously in the younger levels we're calling the obvious along with a good mixture of talking to the coaches but if we have a formation with a QB and 4 runnning backs, it is getting flagged at even the lowest level.

I think that in PeeWee or even 7th grade ball, if you have an illegal formation because some poor kid was supposed to be on the line, and wasn't, tell the coach and let it go. No advantage is being gained here. 7th grade safeties are not reading formations to determine coverages or anything like that.

But if the IF is because they truly have too many players lined up behind the QB, or took an end off the line and sent him in motion, you have to flag it.

If you have enough bodies to cover it. Sometimes at this age level, we're usually going 2-man crews.