the same issue has followed from 13 to 14 to 15: DUPLICATE MINOR-LEAGUE STATISTICS!!!!
This seems to be a carryover issue I addressed last year and so far, its the same players all over again
See: Corky Miller. Has stats for Richmond (AA) and Gwinett (AAA). Richmond was the AAA affiliate for the Braves, but he has Braves AAA and Giants AA stats. The simple solution to me is to either give him Gwinett stats or no stats at all, since coding the Richmond Flying Squirrels will always be kicked by to AA league stats in stats editor, even if you list the league as "2".