baseball question

Pittsburgh at Cincinnati. Bottom of eighth inning. 5-5. 2 out. Runners on 1st (Lopez) and 2nd (Denorfia) . Mike Gonzalez versus Adam Dunn. Dunn hits a soft liner to centerfield, Duffy (the Pirates cf) makes a great diving attempt at the ball, catches it (traps it) after it clearly bounces on the field. Duffy then holds his glove up as if he had caught the ball. The umpire buys it, calls Dunn out. Pirates leave the field. Denorfia scores, Lopez scores.
Umpire conference. Reverse the call. Now the interesting question is, since you reverse the call, what do you do with the runners? The Pirates were leaving the field as Lopez scored.
The umpires award Denorfia home, put Lopez to third and give Dunn a single. Jim Tracy (manager of the Pirates) argues, gets tossed.
Duffy leads off the ninth for the Pirates. On a 1-2 pitch he gets hit on the top of the foot by the pitch. Home plate umpire doesn't award it to him. Duffy strikes out on the next pitch.
Scouting report:
Chris Duffy CF Pirates: Struck out 21 times in 60 odd at bats in spring training. He's in the lineup for his excellent defence. Since he's solid defensively, Jim Tracy bats him leadoff. Jim Tracy is not a dumb man, he just has no other option asides from Duffy. Duffy will easily strike out 150 times this year if he continues to bat from the leadoff position.