I have just encountered a similar problem, the game is asking me to register players before the window closes but there is no 'squad registration' button on the main squad screen. I have downloaded the recent patches (11.1.1 and 11.2.1), but it hasn't fixed it.
I went on holiday for a couple of days, and my assistant manager did a semi-decent job of registering the right players (!), but I am finding that many of the other squads in the league have ended up with the majority of their players left unregistered and therefore ineligible until January. Which is great in terms of me winning the league, but not really very realistic or fair!! Any ideas what is wrong??