Mata, last season's player of the year, was omitted from the squad altogether for Saturday's 2-0 Barclays Premier League victory over Fulham, placing his future under renewed doubt.
Napoli are reported to be considering an approach in January and it has been reported that Mourinho's sparing use of the playmaker has caused friction with owner Roman Abramovich.
"I personally don't understand (why he left Mata out)," Grant told BBC Radio Five Live's Sportsweek programme.
"But in this position Chelsea have so many players, so if Oscar, Eden Hazard, or Willian are out people will ask why they are out of the squad or team.
"Mata was one of the best players in the midfield in the last year.
"A manager needs to take a decision and in this case it's a tough decision. Jose will know how to manage them well."
Asked if Mata had a future at Chelsea, Grant added: "I think yes. He's a great player, he's won games, gave assists and scored goals.
"Chelsea have many players in this position, maybe one more than they need, but that can also be an advantage."
Grant succeeded Mourinho when the Portuguese was sacked in 2007, but his own reign lasted just one season.
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