Whether a player participated in a game is controlled by the game roster. Every game can have a different roster based on the team players by making them active or inactive for a particular game. You can set this is a couple places like the game options - Roster section or selecting from the subs screen the icon showing two players at the bottom of the screen.
There are further adjustments you can make to override this in the report options. From the Reports tab select the Options button in the upper right corner. For season reports you can override the use of the acrive roster for determining games played.