Lineups vs. rosters:
A player who's still on your team, but isn't available to play in a particular game because of injury, etc., should have his or her status changed to "not playing" when you create the lineup for that game. Otherwise, the player's per-game averages stats will not be accurate.
Just click the "playing" status for the player in question when you're entering your lineup, and change it to "not playing". (The status will automatically revert back to "playing" for your next game, so you won't have to manually add this player back to your team after this game is over.)
If you've already got the lineup entered, you can remove the player from the lineup at any point before you finalize the game. (You can do that from the Main Court window, or you can correct the lineup in the Actions window.)
Removing a player from your team's roster (not just from a game's lineup) would normally be done when you're not prepping a game. Click the Players button, and change that player's status to "Off Team" -- you can always easily reinstate that same player later with just a couple of button clicks, if he or she returns to the team.
More details about player status, lineups, and rosters are available in the Players window.
Tip category: Recording games
» Recording games
Tracking fouls during a game
If you get to the game late
» Lineups vs. rosters
Using the Override Scoreboard
Shot Locations, Layups, and Points in the Paint