Hello,
I had some players selected in IS just before an IE... and the MDM recruited me a completely rotten free player to complete my squad. Shouldn't he be next in line? (This was the case for one of the two players selected to replace him)

Yes, your player or players will be back around 0:30/1:00 a.m

I understand the history of selections...

My question is: why did I recruit a free agent to plug a hole in my IE... when I have 18 players available in my squad! Is this a bug?

I don't think it's a bug but rather an action of the game that makes you have 11 holders

Basically, if the selection was made a few seconds before the start of your match and at kick-off you have 10 first-choice players, you'll have the 11th player provided by the game in the reserves and not in your substitutes, even if you have several