It may technically be 'in play' but it isn't necessarily doing anything. For instance "Whenever a runner goes out of bounds on a play from scrimmage, the game clock is started when an official spots the ball at the inbounds spot, and the Referee gives the signal to start the game clock", ( Rule 4, article 2 ). The attacking team then gets the 40 second play clock to control, so for upwards of 30 seconds the ball can sit under the Centre's hand and not moving. Plus, if the QB decides to 'take a knee' that will automatically take another 30 seconds of time off the game clock. ( In theory a team can run out 2 minutes of game time by making this play for 3 successive downs ).
Also, the game clock does not stop after a rushing play that finishes inbounds, again allowing the play clock to eat into the nominal 60 minutes of playing time.
( You have read the rules ? ).