I don't know the rules enough to know about the illegal formation but it's sus that we didn't get a number and the announcers didn't see it either.
The penalties today were on players that weren't planned starters and the sooner Buffalo gets Brown, Feliciano and Ford back, the better. This is a year with no preseason and TC, so teams that have major changes tend to have it rough. In Buffalo, this is a major reason the defensive line isn't good right and may be contributing to the run blocking woes, as well.
I also wonder if a part of the running game is part of building the team for Allen to succeed. He's largely a shotgun passer, and really prefers empty sets. Honestly enough.