The Trotters boss, who praised the home side's performance after coming from a goal down to take the lead, insists that the visitors should have made their opportunities count earlier in the contest.
"We started the game well, got in front and really we should have put our foot down at that point," he told the club's official website.
"We had wave after wave of attacks, passing and moving the ball and creating plenty of opportunities. On another day, Ivan Klasnic would have had at least a couple of goals to his credit.
"To be fair, their goalkeeper had a good game too, making a number of decent saves. Credit to Macclesfield and how they approached today's game because they were positive and looked to get forward as often as they could."
Bolton return to Premier League action with a trip to Old Trafford next weekend.