The 26-year-old, who spent 10 weeks in prison over the summer, was not selected for the 1-1 draw at Stadium MK, with Brown refusing to divulge the nature of his player's breach.
"Nile isn't involved because of a disciplinary procedure yesterday," the 58-year-old told the Southend Echo.
"It's not for public consumption what's happened, but it's just down to discipline and we'll leave it at that."
However, Ranger posted an update on social media after the game suggesting that lateness was the reason, claiming that he has "to work on my time keeping".
The former Newcastle United forward has played 14 times for the Shrimpers this season, having missed the start of the campaign due to a stint in Pentonville Prison for online fraud.