Thanks for the report! Here are my comments:
* As you predicted, penalties are from experience + discipline. There is a measure of fatigue and crowd noise (which is in the sim although there's no record of it) as well.
* I think you linked to the wrong play for the mystery "tackle" - I think I know what you're referring to, though, but I haven't gotten to the bottom of it. The QB for some reason just doesn't know what to do.
* The starters get pulled in pre-season, which is pretty much everyone in the #1 spot. So that probably explains how you ended up with your #1 receiver not having very many catches, and if your depth chart didn't go deep enough then your kick returner would have made it onto the field. You can control when your starters are pulled via the Misc Gameplan options screen. It could also
be fatigue-related - first pre-season game, players are not fully conditioned, and will not be on the field as consistently.
* Interesting on the injuries. I'll have to look to see if there's a threshold for showing/not showing injuries in the game log, I don't recall offhand.