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Assistant boss David Kerslake felt the Gills should have been awarded at least one penalty against Charlton.
Leading 1-0 and moments after Stuart Nelson had saved a Ricky Holmes spot-kick the Gills had two appeals for a penalty themselves.
Both were turned down and Charlton scored their equaliser from the spot in the final minute.
It meant for a frustrating day on the sidelines.
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Kerslake said: “I didn’t think their first penalty was one in my opinion. I thought the boy jumped and fell on the floor. I have had a look at it afterwards and I stand by that.
“The referee had to give their second one. Herd, unfortunately, has gone up and led with his arm, I don’t know why, but he has done it and it’s a penalty.”
Match Report: Gillingham 1 Charlton Athletic 1
Asked about those not given for the Gills, he said: “Certainly the first one could have been given but the second one, when Cody goes through one versus one, that in my opinion is a stonewall penalty.
“I was thinking, ‘here we go, 2-0’ and I couldn’t believe it when it wasn’t given. It was a tough one to take.
“I spoke to the fourth official after the incident. Both he and the referee said they knew there was contact but didn’t think there was enough to give a penalty and that was very disappointing.
“I didn’t agree with that assumption. I knew there was contact, it was enough and it was a stonewall penalty.”
The Gills could have led 2-0 but instead Charlton piled the pressure on and got their reward, from a game they had been second best in for long periods.
Kerslake said: “We were outstanding in the first half and the first 15 minutes of the second half, we were well on top, they rarely entered our half.
“Unfortunately we haven’t been able to see the game out and we have paid for it again.”
Asked if the Gills’ were suffering from a lack of fitness late on, the assistant manager said: “It is not down to fitness, it is quite difficult, the manager shouts from the sidelines ‘step up, step up’ but it is a natural thing that players do drop off, you will see it at all levels.
“It is something we work on in training. I thought the second half performance was okay, it wasn’t as good as the first, but it was okay for 20-25 minutes.
“You expect they are going to throw caution to the wind, they had changed shape and full-backs start to bomb on. You have to see the game out.
“I didn’t see them scoring, I really didn’t, but unfortunately there has been a penalty and that’s how they have taken the point.”