This problem has existed since at least OOTP 11. I keep hoping it'll get fixed one day. I feel like I reported it in previous editions.
Often, when managing a minor league team (this time I'm playing a historical league, but I've also seen it in fictional leagues), when you get an email about players getting shuffled around, the email will be incorrect; players it says you lost you'll still have, players it reports you received you may not have, and you may sometimes have new players you've never heard of.
As an example, here's a case where it told me that I got Rezzori and lost Ruiz; note that I don't have Rezzori and still have Ruiz.