It is the second week in succession and also a third occasion in his last four events McIlroy has sat out the weekend rounds.
The 41-year-old's effort comes just nine days after booking a spot for the British Open by finishing second in a qualifier at Woburn, and he will return to Royal Birkdale next week, where he finished second in 2008.
"I'm frustrated but, at the same time, I thought I saw some good signs out there", he said, trying to take something positive out of his latest early exit. She says it's the only five hours of the day when I am the boss.
"It's hard to sort of put my finger on it".
"One more tournament isn't going to change you and I'd hate to be that guy".
After opening his second nine with back-to-back birdies as well, Howell made six pars and sank his longest putt of the day from 26 feet for a birdie at the par-3 seventh.
"Look, it is what it is and I just have to get myself ready for next week. I've been playing well this year and everything has been trending in the right direction, being in contention at the first two majors", he said. "But I felt like I learnt a lot over those two days that I played".
The 28-year-old missed two straight cuts in 2015 before bouncing back with a top ten at the US Open, so perhaps all is not lost with regard to Birkdale.
The resulting double bogey was at least followed by a first birdie of the day on the par-five 14th, but another bogey on the 18th, where he pitched into a greenside bunker, took the four-time major victor to the turn in 40.
A share of 17th in the Travelers Championship was then followed by another missed cut in defence of his Irish Open title at Portstewart, but the four-time Major champion believes he is not far away from a winning display. "I feel like I've just been on the wrong side of them (fine margins) the past couple of weeks, and hope-fully next week I'm on the right side of them". I know I'm saying the same things every week at the moment, but hopefully next week I can say I stayed patient and it all worked out.
The latter, who is a two-time Challenge Tour victor, made seven birdies, one eagle and just two bogeys to sign for a magnificent seven-under-par 65, leaving the 28-year-old in prime position to break his duck on the European circuit.