Substitute Ashley Fletcher struck late on to earn Barnsley the spoils and condemn Rovers to a fourth straight defeat.
However, Ferguson felt his side merited something from the game.
He said: “Maybe a month ago we might have nicked that 1-0 but at the moment you lose it 1-0, and really I didn’t think we deserved to lose it.
“I thought Barnsley were better than us in the first half, they counter-attacked on us well and Adam Hammill gave us a problem.
“But I thought when Mitchell [Lund] went to that wing back position he did well. He played well.
“It’s another disappointing result though. We’re on a bad run, there’s no question about that. We need to get out of it.”
Rovers, at least, improved on last weekend’s shocking display against Sheffield United.
“I thought we battled away quite well,” said Ferguson.
“It was a better performance than last weekend and in the second half I thought we got control of the game.
“We had a lot of controlled possession without threatening too much. Probably our best two chances in the game fell to Mitchell Lund. We thought we had control when we lost a really poor goal.
“In the first half we played too many long passes, which we didn’t want to do. We wanted to hit diagonals from our centre halves but we hit too many. We wanted to shorten our game up and get control of possession, and we did that second half and we did it well. I thought we could have been a bit more threatening with it.
“But that’s what happens when you’re on a bit of a bad run, you lose games like that. But I don’t think we should have.”