This happened to our team last year at Triple Crown World Series. We were the visiting team in the top of the first inning, two outs runner on second, base hit to outfield runner on second tries to score and is thrown out on a bang bang play. We go start warm ups for the bottom of the inning. Our coach sees that third base is futher back than second base. We call the upms over and they look at thebases and agree, but they do not know what to do. We call tournament director over( naturally we want to repaly the inning) but he said to finish the inning then move the bases.
My question is, was this the right call?

www.banditosbaseballclub.com

Go Hard or Go Home

All things being equal it was probably the correct call.
Avoiding the whole conversation such as; how come neither team noticed it when taking infield, or the coach in the 3rd base dugout, or the 3rd base coach,etc. without bringing it to someones attention.
There are no "do-overs" in baseball. This way both teams played their inning with the same advantage or disadvantage of the base being in the wrong position.
This is why when turing lights on at a field, try to have it done at the end of an inning, thus giving each team the same advantage of having the lights on.

Yes, it sounds right to me. There are a number of things in sports (not just baseball) that are assumed. Is the pitchers mound 60'6" from home, is the mound no higher than 10", are the bases right, is the hoop actually 10' off the floor?

When these things are found out the only fair way is to continue the inning so that no team
had an advantage. Once that inning was completed, call out the crew and get it fixed.

I umpire on a lot of fields for HS, Legion and Youth ball that are not much better than sandlots. We try and walk off the distances, but its just a guess.

I only mildy disagree with Pirate fan on turning on lights. I see that as a safety issue and that falls under my judgement, I never know how long an inning will go, so waiting until an inning is over is rarely considered.