Connolly said he was concerned about the centre clearances, an area the Bombers totally dominated throughout the match.
"Well the clearances probably underpinned everything, we lost 36-18 and it's a huge issue," Connolly said.
"You always look at it positively that if we can rectify that situation we will go inside 50 a lot more and have a lot more scoring opportunities, but we just haven't got it right. So we'll go back to the drawing board again."
The win keeps Fremantle in touch with the top eight, and Connolly admitted it lifted some of the pressure off the team.
"There would have been a little man in their head saying 'gee, if we don't win this game it really makes it difficult,' and they dealt with that," Connolly replied when asked about the thoughts of the players entering the match.
"The guys stayed focused on the task."
Midfielder Paul Hasleby was in doubt for the clash early in the week with a mystery injury but made a welcome return to form with 27 disposals.
"I think our medical staff and our conditioning staff have worked hard to put their finger on the problem and I think we have found what it is, and obviously I'm not going to tell you," a tight-lipped Connolly said about his star player.
Ryan Murphy was a standout in the forward line and kicked four goals, and Connolly praised the 21-year-old.
"It was a big step forward for Ryan, I think it was a positive step," he said.
"There's so much more improvement left in him that he's going to end up a very important player in the future for us."
Ryan Crowley was another to impress with four goals to complement his 13 disposals after earning a late recall into the squad.
"He's played very good football when he's had a good role in the midfield," Connolly said.
"He's got some tremendous strengths to his game. He's a big guy; he's got great running ability and he's got good goal sense. He's given us that type of return on the scoreboard playing on quality players a few times so it was a very important game for him, and us."
However, Connolly warned the two youngsters not to get complacent with their performance against the Bombers.
"It's been a solid win and we've got a big game next week and there'll be a lot of publicity around that, and Ryan Murphy's kicked four and Ryan Crowley's kicked four," he said.
"I just stress that it's such an important challenge for them this week to keep focused on the basics because if you don't you'll get eaten alive next week by Collingwood. So it will be interesting how those guys respond after their performances tonight."
Josh Carr and Paul Medhurst will face a race against time to prove their fitness for the clash against the Pies next Sunday after both sustained calf injuries in the win.
