Situation Critical!!

[JJ]

Well, it's not really THAT bad, but it got YOU here...

All codes. R2, outs don't matter. Passed ball, R2 advances to third base and rounds it. F2 runs back to the screen and picks up the ball, then throws behind R2 at third base - and nails him (edited to say "throws him out").
Here's the kicker -
Here comes R2's coach from the dugout and he tells U1 that the ball the catcher picked up wasn't the game ball - "There's the game ball", he says, and U1 now sees a SECOND ball on the ground about a foot from where the FIRST ball was picked up by the catcher.
Oh-Oh!
NOW what do you do? U1 was not aware of the second ball until it was called to his attention. U2 wasn't, either, but he thinks the ball the catcher picked up was in fact the wrong ball.
Rulings/educated opinions, please?

JJ