Two different sentences there. Let me break it down for you:
1) There were numerous times when HHS ran offensive plays with only 10 players on the field. The refs never saw it though. HHS had to burn several timeouts, but there were plenty of plays were the refs and HHS coaches were clueless.
2) The play where HHS broke the huddle w/ 12 men and then called a timeout before a penalty was called or a play was run, should have been a penalty. You can't save a "breaking the huddle w/ 12 men" penalty by calling a timeout. It looked like GQ and Co. were pointing out the penalty to the stripes (during the timeout), but the officials were too stubborn to admit their mistake.
Clear as mud now, right?