Winger Mark Duffy was sent off after 31 minutes when the referee ruled he led with an elbow on Shakers player Patrick Clegg.
“We never saw the red card incident and the ref seems to be the only person who did," said Knill, who returned to Gigg Lane for the first time since quitting his role as Shakers boss a year ago to take charge at Glanford Park.
"Speaking to everyone, they thought it was soft. I think everyone was shocked when he pulled the red card out – it's one of those again
“We're unbeaten this month despite another game when we were down to ten men. We're quite well drilled in it now. We know exactly what we're doing and the shape is strong and compact so it forces the opposition to go long.
“We look tough to beat and credit to the players because it's been an unbelievable month."
The point helped keep the Iron just ahead of the relegation zone, with a four-point gap to them and Walsall - who were denied a valuable win at Sheffield Wednesday after conceding an injury-time leveller - in 21st.
“I'm glad it's the last midweek game. We've got plenty of tired legs and bodies but the effort is there for everyone to see," added Knill.
“From where we were to where we are now is a vast difference.”
Bury struck the woodwork twice in the first half through Shaun Harrad and Efe Sodje.
The home side have not won in their last 12 games to drop back into the relegation dogfight, but boss Richie Barker was relieved to get a point after three consecutive losses.
“It's not ideal but it's stopped. I can't fault the players for their effort or determination because they've given me everything," he said.
“We've hit a post, we've hit the crossbar and we've had probably two cleared off the line. We can only do our best and I felt we certainly deserved to win. I think the sending off actually affected us because we were the better side until then.
“What it did do was enable Scunthorpe to just try and get something out of the game. We should still be doing better but we created enough chances to win the game."