After some restarts to understand the issue clearly, I found that the friendly match with second XI generates this second B team, but it's not then scratched.
After the database update in March, Portuguese teams that have a B team, now have a second B team. They have separate games, separate squads, separate everything. Can this be fixed? It's a mess in inbox as well to understand which B team it is since the second B team has friendlies all the time. I see this in all teams that start with a B team in Portugal. These B teams in Portugal should work as the ones in Germany.