The fans were not happy that Larkin was the player removed but Gray says injury was the reason.
"Maybe the ones that disagreed with my decision didn't realise Colin was injured," said Gray, who also lost top scorer Adebayo Akinfenwa to injury in the pre-match warm-up. What made my mind up was that he was limping when he was running around.
"He's got a very bad dead leg and it'll be touch and go whether he plays against Swindon tomorrow night.
"That was one of the reasons for the substitution. Not having Bayo either and losing Giles Coke before the game I had to switch things around a little bit.
"Bayo just tweaked his hamstring and that could have happened at a minute past three and we would have had to use a substitution. But like Colin Larkin he's a doubt for tomorrow night as well now."