The most common ways of dealing with late players are:
Make them run laps or do extra conditioning
In more extreme cases, cut their playing time
There is an alternative!
Arrive a few minutes earlier than normal for practices. Set-up a small-sided field within your practice area. As players arrive, hand them pinnies and let them scrimmage.
This accomplishes several goals:
It rewards the players that are early and on time, rather than penalizing the ones that are late.
It gives you, as the coach, time to set-up your practice while the players who are there are constructively occupied and getting extra touches on the ball.
It serves as an effective warm-up.
It gives players an extra chance to do what they enjoy most – PLAY!