Bunn, on loan from Blackburn, superbly kept out a Gylfi Sigurdsson penalty and also denied Ivar Ingimarsson and Shane Long.
Chris Morgan stabbed home with 10 minutes left to put the game to bed, but Blackwell knew the scoreline flattered his side.
"If it was a school report, it would be 'could do better'," he said.
"We started so well but I felt that we just took our feet off the pedal. It became too easy and we were too sloppy.
"They are a team full of Premier League players but you have got to beat teams like that.
"In the end it was thoroughly professional but I would like to have seen certain things done better."
United have gone six games without conceding at home and with just one defeat in 11 Championship games, Blackwell is confident his side can maintain their promotion push - providing they keep all their players fit.
"We have got nine games in February and loss of players has been our Achilles heel this season," he said.
"I am aware that we are slightly short, but we we are starting to get a settled unit.
"I think we have got a squad of 15 or 16 that is comparable to anyone else."
Reading caretaker manager Brian McDermott was in no doubt that missed chances cost his men.
"(It came down to) chances they took and we didn't. They have had opportunities and scored the goals.
"We have to defend better. That's the story of the game.
"The keeper has been good all night and made good saves. But if we keep creating the chances, I am convinced they will start going in."
McDermott has guided the Royals into the last 16 of the FA Cup under his temporary tenure, with victories over Liverpool and Burnley on the way.
But it is a different story in the league, with his side in the bottom three and facing an uphill struggle to stay in the division.
"We need big hearts. We have 20 games to go now, we are where we are," he said.
"It's a massive challenge for all of us, and we are up for it."
Speaking on his position, which he feels he has done enough to make permanent, he added: "I will be speaking to the chairman this week.
"He texted me before the Burnley game but I have not spoken to him since then."