Neal Bishop's first half header was the difference between the two sides as Rovers disappointed at Ewood Park.
Speaking to Radio Rovers after the match the Rovers boss said: "It is massively disappointing. There are no excuses, it wasn't good enough.
"In the 12 months I've been manager that is the worst that it has been.
"I'm not accepting that, not working as hard as what we have done for a performance like that.
"Credit to Scunthorpe, they put a decent performance in, but for 45 minutes it was nowhere near good enough for us, not with the standards that we've set.
"It was just not acceptable. It isn't what we are about. The second half we had more of a go, but it is a lesson for one or two of them in there."
Rovers are back in action this Saturday when they travel to Bloomfield Road to take on Blackpool.
Tickets for the match have all sold out, so why not listen to full match commentary on Rovers Player