Here is a thread about debuting players. No one mentioned Miguel Vargas’s debut so he was not linked up before his debut.
If you see a red X, no matter if the player is actually in the lineup, they will be benched and we will not manually change that. Vargas had a red X because he was not manually linked up before his debut.
There are a huge number of moving parts in terms of player debuts and also autobench. When those two systems intersect, weird things will happen.