If you haven’t made any manual changes to your team ahead of the next matchday, and any of your outfield players then plays no part in that matchday, the game will try to sub out the inactive players for players on your bench.
When you save your team ahead of each matchday, you’ll select the priority order of your outfield subs. Then, if one of your starting players doesn’t play a single minute that matchday, he’ll be subbed out for the highest-priority player on your bench who did play that matchday, and whose substitution doesn’t break the formation rules (minimum 3 defenders, minimum 2 midfielders, minimum 1 forward).
The same process applies to your goalkeepers.
Automatic subs happen once a matchday is finished. If you’ve made any manual substitutions or changed your captain during the matchday, no automatic subs will be made.