http://iscoresports.com/

Runner at 1st, no outs. Fly ball for a 1B to LF in front of fielder. Fielder misplays the hop for an error- runner from 1st scores, batter advances to 3rd.

How do you score the 1B then the advances by runners on the same play without it being recorded on next batter's AB?

Set the Minimize Questions option to NO and you will be asked about each runner after entering the single (including the batter) so that you can account for situations like this. See the Minimize Questions setting in the following section of the iScore documentation:

http://iscoreleagues.com/manual/#h.2q4k99qxrzsl