Odd Call And I Don't Understand It.

A couple of things :
1) Potentially, the penalty was not even called on the OLB you saw, and a different defender made the illegal block below the waist. 
2) In the judgement of the official, the RB clearly was not a ball carrier, and therefore the OLB's contact against him violated the blocking below the waist rule. 

I don't recall seeing officials announce the player who committed the penalty to those in the stands in HS ball.  

It isn't about being helpless.  I am no official, but it sounds like in the official's opinion, the RB clearly was not a ball carrier.  It is illegal for anyone to block below the waist under federation rules unless the players involved meet the free blocking zone exception.  A RB, and a LB would not on the play you describe. 

True, but if he was carrying out a fake he can still be tackled, same as any ball carrier. Just depends on how long after the fake the hit occurred.

No you can't tackle a potential future ball carrier. However there is a weird loophole. A few years ago our league went gaga over shovel stuff. And it was a real bear to defend so it came to be a popular base play. But then defenses got smart and when you ran it on 1st and 10 they would just tackle the RB. Spot foul at the LOS and an automatic first down.

The coach asked the official who the foul was on and that was when he told the coach. There weren't that many people there so it was easy to hear. I could see it if the LB would have just hit the RB when he was nowhere near the play. But he him during the mesh during the read. I guess it would just come down to a judgement call by the official.

They've also begun to call all numbers on all penalties this year or last.

This is simple, the Ref messed up (assuming the OPs info is correct).

Week 9 we played at a place that had the refs miked up and they announced numbers.

I need clarification.  Was the ball faked to the RB or was he just a potential ball carrier? 

Really, the ref doesn't know the rules? That's like me saying you, as a coach, doesn't know how to call an offense.

The OP doesn't state that there is a fake to the RB, therefore, the ref properly identified a foul for an illegal block below the waist. With the information contained in the OP, this is the correct call. 

Based on the OP this call would likely be made by the Umpire or the white hat. As an umpire, I try to keep track of my linebacker's numbers. I do this to see if they are cut blocked at by a lineman or if they block low on a RB. The white hat does the same with the RBs. 

As far a who should call what fouls on a field there is a general mechanic of "not fishing in someone else's pond." This usually means that we are not going to throw a flag for a foul for something that is not in our zone. However, there are some things that we will throw flags outside our zone. Usually this related to a safety foul. For example, you mention an umpire throwing a flag for a late hit out of bounds. As an umpire on a play going out of bounds I will be heading towards that area to help retrieve the ball and to clean up while the flank official is getting the spot and moving the players back onto the field. As I am moving towards the sideline I may have a much better view of the foul. Also since this is a safety foul, I am going to throw it. 

A flank may throw a flag on a holding call because their responsibility on a running play is to watch the blocks occurring in front of the point of attack while the R is watching the ball carrier. As for the R throwing a flag of DPI, I can't explain that. 

Not necessarily, especially when the OLB took the RB and the CB (cornerback) took the QB. OP said the OLB was the read key. Usually the DE is the read key in zone read. That certainly implies to me that the RB was the pitchman and a potential ball carrier instead of someone who was faked to like on zone read.

I am taking the word “read” to be “option” here. Sometimes terminology is different for people. I could be wrong. That is why I asked for clarification.

If its a mesh type play; power read, or dive option, or zone read (could be any of those based on the OP description), then it sounds like a bad call to me. The OP makes it sound like a bang/bang type of situation, and the RB would be appearing to have the ball. However, if its a speed option look then it sounds like its the right call. Although like ANY discussion on here about rules, nobody will agree on anything without video to see.

no.. I think it fits perfectly... keating is going all the way to make the assumption that this ref in the situation doesn't know the rules.. and he is just a typical guy who doesn't know the rules.. based on one play that may or may not be right (no real way to tell with out watching)
very similar to assuming a coach is an idiot based on one play call