Along with the new depth chart system in place for 2.x, there is also a team profile that is used for each team.
The team profile is used not only to set up the draft, but also to indicate how many players in each position the coach wants to keep on the roster. When the final cut down comes from training camp, these roster numbers are used to cut players that the coach has not done manually.
The roster numbers are maintained by the AI, so if free agent changes are made to the team, or some players become inactive by injury, one should make sure that the roster numbers match the roster. If not, the AI will automatically make roster changes that can include depth chart changes.
If a team drops a receiver and picks up a receiver, there won't be a problem, but if a team picks up a receiver and drops a defensive back, it could cause depth chart changes or a roster notice to come up when trying to enter a game.
The key here is maintaining the roster, roster number, and depth charts for human controlled teams.