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Captain Lee Martin lasted just 45 minutes after returning from suspension.
Gills manager Steve Lovell said he was forced to take the skipper off at the break due to illness.
“He came back and he had a chest infection,” Lovell said, explaining his half-time substitution.
“He wanted to play and give it a go, but at half-time he was in no fit state to carry on but he will be back to normal next week.
“He had a go and he is a great character, we need him around. He struggled because of that chest infection but he will be back.”
The Gills were also without vice captain Gabriel Zakuani, who missed the game with a head injury, picked up against Rotherham in the week.
Lovell said: “Gabs will be back (for this Saturday’s game against Bristol Rovers).
“We will mull over it, see how Bristol play and put a team out next week to put right what went wrong here.”
The Gills boss will address Saturday’s performance with the players today (Monday).
He said: “At the end of the game there was nowhere to start, there was no point ranting and raving, I would be there until 10pm.
“I just said we’ll see you Monday and discuss it then, where we can all sit down and reflect on the day and be positive about the week ahead, going into Saturday.”