Since, Wyoming's RB was wrapped and driven backwards 5 yards (forward progress was stopped) the refs blew the play dead. This was the right call.
As contrast look at Hill's second TD. The play wasn't blown dead when the DB wrapped up Hill, because he didn't stop forward progress. Again this was the right call.
Now back to the penalty on Ben. The whistle had blown before he engaged, the refs absolutely had to throw the flag when he finished that tackle. If Ben doesn't finish that tackle there is no flag.
They should have called the non interception/incomplete pass dead when the ball hit the ground, and long before a penalty occured. That one felt like they were waiting for a penalty so they could help Wyoming come back. Once it was determined incomplete the refs should have picked up that flag. This play was a far more embarrassing mistake. There are plenty of other examples of bad penalty calls and no calls that make a better argument of how incompetent these refs are.