Okay, let's clean up the terminology a little... R1 was on 3B, R2 was on 2B, R3 was on 1B. It'll help you a lot on this forum.
Back to the OP. This is where I tell the runner he's full of sh1t. If the ball was caught, he's out. If the ball WASN'T caught, he was out anyway for passing R3. So in either case, he was out. We now have 2 outs.
Since he then hindered the defense's ability to make a play on another runner (R3), the runner closest to home (R1) is also out (ASA 8-7-P). Three outs. No runs score.
It's not up to the umpire to scream at the top of their lungs whether or not the ball was caught or whether or not someone was out. We do our best, but sometimes, the crowd gets a little loud, or runners get a little deaf (either intentionally or otherwise).