Bases at wrong position?

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.