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The defender was a surprise omission from the XI at Swansea, having contributed to a clean sheet against Wrexham.
Carter was brought on at half-time with Tom Atcheson struggling and Rovers 3-0 down. It was the fifth successive game in which the centre-back set-up has been altered.
Mowbray confirmed that it was a fitness decision on Carter, with games at Ewood Park against Stoke City and West Ham coming up.
"We know Hayden really, really finds it difficult to play two or three games a week," he explained.
"He can get through 90 minutes, but if you ask him to play again on Tuesday, he'd probably break down, and then we'd be out without him for eight weeks.
"So I'm trying to manage the players we've got, manage the group we've got and that's the reason really.
"I think I've got choices and I think every coach wants choices and decisions to make, and mine are a little bit easier to make because two of our four central defenders definitely can't play three games a week.
"They have really struggled to play two games a week without getting injured for months."
Rovers' setback against Swansea was frustrating for Mowbray, who felt his side didn't do basics well enough. They played into the host's pressing traps and didn't play the percentages enough.
It was disappointing after a great win against Wrexham, with Rovers still trying to find consistency in a difficult league.
"We're always striving for consistency," Mowbray admitted.
"I generally think the best version of Blackburn Rovers would have come here and given them a really good game. We didn't give them a good game, it was too comfortable for them.
"What do I talk to them about? I'm not a screamer and a swearer and a shouter, but I had 20 years as a football player and I had 22 years as a football manager.
"I can talk to them about emotion and what it takes to find consistency. Because you win a few games doesn't mean you're a great team, you haven't achieved anything yet.
"So I just remind them about basics, and if you don't fight, if you don't compete, you aren't going to win very much in your life.
"My frustration is that we've watched and we've seen what they do, number one you give them all the data, give them all the stats, and yet we didn't really heed it.
"We were still wanting to play out, you know you get stuck in how you play, what you do, and if you'd have seen some of our football this year it's been pretty good.
"But against that intensity we really toiled, really struggled, didn't get over the halfway very much, never mind threaten your goal."