His errant driving, for one; two triple bogeys he encountered on Thursday, the first time that has happened as a pro; and failing to scramble well when he missed greens.
Koepka raced out to nine under early in his second round, but dropped two shots on his back nine on his way to a 70.
Fleetwood has made the cut in just one of his seven major appearances to date, but the 26-year-old from Southport made an ideal start with a birdie on his opening hole and added four more in a brilliant putting display.
The 44 under-par rounds broke the first-round mark of 39 at Medinah in 1990.
England's Paul Casey is a shot further back on 7-under after carding a 71 to follow up yesterday's 66. They were joined by Harman and Fleetwood, who each had a 70.
It was a nice comeback for Casey after he triple-bogeyed the par-5 14th and shot 38 on his first nine.
"Not every day you enjoy a round of golf with an eight on the card, but I'm a pretty happy man", said Casey afterwards. "It was a bit of a roller coaster".
"Even though it's very disappointing to not be here on the weekend, I think these last two rounds will serve me well going into the summer, " he said.
Tall fescue grass on the fourth, 12th, 14th and 18th holes was being cut on Tuesday as McIlroy gave his pre-tournament press conference, which caught the 2011 champion by surprise.
The last six majors have been won by first-timers, and that cycle has a good chance to continue.
None of the leaders had as shaky a stretch as Casey, who made 8 on the par-5 14th hole - after hitting into the fescue and almost whiffing on his swing to get out - and bogeyed the next hole. Johnson came in with 73, but that was not almost enough, as he finished at 4-over 148 when 145 or better was needed to advance.
Sure, he birdied four of his last six holes to salvage a 71 and finish at 5-over 149. "I don't know that I've ever played a US Open where I've had that much enjoyment". No matter how fast you start or how many birdies you make, the pars are the ones that keep you in it. Cameron Champ, who just finished his junior year at Texas A&M, birdied his last hole for a 69.
He then bogied the 15 hole, hitting it short of the green in two and failing to get the up and down. "You've got 156 of the best players in the world here, if we can't hit it within that avenue, you might as well pack your bags and go home".
A crowded leaderboard missing most of golf's big names has set the stage for a wide open run for the U.S. Open trophy as third-round play got underway on Saturday at a steamy Erin Hills.
Harris English is 4 under after a second-round 69.
English says "They want par to be a good score, and this afternoon it will be".