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Tom Eaves was taken off before half-time on Saturday but Gills boss Steve Lovell said he could have subbed anyone.
Gillingham conceded twice during a poor first half at Bury, prompting Lovell to make changes.
While he switched formation, he also took leading goalscorer Eaves off, replacing him for Conor Wilkinson shortly before the interval.
Lovell said: “I felt that Tom was perhaps having one of those games, where nothing was going right for him. That was the only reason, it was a tactical one as well, he wasn’t getting in the game.
“It happens and to be honest any one of the 11 could have come off in the first half.”
Eaves went straight down the tunnel after being substituted. “I spoke to Tom and he is fine,” added Lovell.
“I make decisions on what I see, sometimes they come off and sometimes they don’t. If we had scored at the end it would have come off.
“Tom has been great for us, he has worked hard and he will be my first name on the team sheet every week. Just because he has come off doesn’t mean he won’t be playing next week because he has had a good season.”