I have checked all players in Master League Mode and I found in total 25 duplicates.
8 of them are created by Konami - the same player exists twice in different licensed teams:
1.) Xisco in Ossasuna (correct) & Mung Thong United (wrong: was old team)
2.) Robson in Boavista (correct) & Esthegal FC (wrong: was old team)
3.) S. Garcia in RCD Espanyol (correct) & Al Rayyan SC (wrong: was old team)
4.) R. Doan in Groningen (correct) & Gamba Osaka (wrong: was old team)
5.) Leo Bonatini in Wolverhampton (correct) & AL Hilal FC (wrong: loan to wolverhampton)
6.) J. Valdiviva in Colo Colo (correct) & Al Whada FC (wrong: was old team)
7.) Ahmad Yasser in Cultwal Leonesa (correct) & Lekhwiya SC (wrong: was old team)
8.) A. N'Diaye in Clermont Foot (correct) & Aal Taawon FC (wrong: was old team)
For the Moment I will keep the Players and Teams like they are.
Simply releasing them from the wrong team would correct those 9 rosters, but still the players are there in Master Leagu Mode, maybe someone has a smart solution to fix this issue - live updates have not chenged that by now.
The other 17 players I have found were in:
Hamburger SV (2), Qarabag(2), Apoel Nikosia(3), Maribor(1), Celtic(2), Partizan(1), Santa Fe(1), Medellin(1), Chacarita(3), Melbourne Victory(1).
Here is a fix to remove the duplicates. I transferred the from the beginning existing ones and resetted the used ones and released them from each team.
Simply Import those Teams with 2nd and 3rd box ticked.
Maybe valencia5 or someone else can double check the players and find out if there are any duplicates left, besides the 8 KONAMI ones mentioned above.
And here is another fix / update for V1.1:
https://www.mediafire.com/file/5bz6hjfhdz2duo9/Fix for V1.1.rar
This Update includes 3rd kits for Premier League and a fix for Sunderland (Credits to Erzo77). To install these files, just tick 3rd box when importing the teams.
Also included is an update of African Nationteams, modified by nicoultras.
To install this files, delete in EDIT Mode following 5 STADIUM images first:
Then import the files ticked with 2nd and 3rd box ticked.
What I did last year was put all the "Konami" duplicates on one of the created teams, and reset some of the unused free agents that were overwritten to be added to the created team. And use the Konami "hard" duplicates so to say...as players to be over written, then export the new created team, with the hard duplicates being overwritten/edited. Keeping only one instance of each Konami duplicate. This will eliminate the hard duplicate from whatever OF is exported.