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Is something wrong with the Patriots?

These three fatal flaws could put an end to New England’s repeat title hopes.

NFL: Houston Texans at New England Patriots David Butler II-USA TODAY Sports

Let’s get this straight right away. The Patriots are still a dangerous Super Bowl contender. Any team led by Tom Brady, even at age 40, would be.

But the 2017 New England team looks more vulnerable than the odds-on preseason betting favorite ever should.

On Sunday, the Patriots squeaked by a flawed Texans team at home, needing a 75-yard touchdown drive in the game’s final minutes to put away a team that came to Foxborough as a 13.5-point underdog. Houston scored 20 points in its first two games combined. In Week 3, rookie Deshaun Watson led his team to a 33-point explosion that threatened to fire up the Northeast’s hot take machine.

Although Brady and the Patriots offense — even while his receivers have struggled to stay healthy — have found a way to win, a struggling defense and a low-efficiency running game have sunk the team’s ability to crush opponents down in the second half.

The 2017 Pats have yet to prove they can grind down the clock or stop opposing quarterbacks from lighting them up downfield. And while three weeks into the season may be too early to start worrying in earnest, there are three big problems that stand to derail the club’s Super Bowl aspirations.

1. The Patriots running game has been woefully inefficient.

Mike Gillislee has proved to be a capable replacement for LeGarrette Blount at the goal line after scoring four touchdowns in his first six quarters with the team. Otherwise, the team hasn’t moved the ball efficiently on the ground.

The Patriots rank 22nd in the league with just 3.5 yards per carry. What’s more troubling is their inability to convert key short-yardage situations. In the season-opening loss to the Chiefs, Gillislee was twice stonewalled on fourth-and-1 carries up the middle. On Sunday, the Texans stopped him again on third-and-1 in the fourth quarter of a game New England trailed. The impact was significant — when the team faced third-and-short on its very next drive, offensive coordinator Josh McDaniels dialed up an unsuccessful passing play instead.

It would be easy to suggest the absence of Blount is the cause for these problems, but the Eagles haven’t been utilizing the 250-pound bruiser as their money down back. In Sunday’s win over the Giants, the team mostly deferred to Carson Wentz sneaks and carries from the much smaller Wendell Smallwood on third- or fourth-and-short. Blount has converted only one of three third-and-short opportunities this fall — though his 4.3 yards per carry so far in 2017 would be tops among all New England tailbacks.

The Patriots have never been the kind of team to rely on one workhorse’s back, but Gillislee’s inability to regain the ultra-efficient ways of his past (5.7 yards per carry playing behind LeSean McCoy in 2016) have limited the New England offense. That’s put even more pressure on Tom Brady’s golden arm, and that could be a problem because ...

2. The Patriots’ offensive line isn’t playing up to its 2016 standard.

The return of O-line coach Dante Scarnecchia transformed the fatal flaw that bounced New England from the 2015 AFC Championship Game into one of the team’s biggest strengths last season. Marcus Cannon went from being a cut candidate to an All-Pro. A rookie third-round pick, Joe Thuney, emerged as one of the most valuable guards in the league.

Scarnecchia had all the same pieces in place for 2017, but the product has been a cheap imitation of last year’s output. After being sacked on 4.5 percent of his dropbacks a year ago — a mark that ranked sixth in the NFL — Tom Brady has been sacked on 8.3 percent of his passes. Through three games, Brady’s been sacked 10 times and hit 20 more, two figures that inspire sweaty palms for fans of a 40-year-old quarterback.

Brady has found a way to overcome that pressure and lead the league in passing yards while ranking second in passing efficiency. He showed off a developing rapport with Brandin Cooks, who is emerging as the team’s best deep threat since Randy Moss (25.6 yards per catch). However, he’s also got a cache of receivers who work best when given time to flash upfield — Cooks, Chris Hogan, and Phillip Dorsett are better as deep threats down the sideline rather than slot receivers on short and intermediate routes. But the collapsing pockets that have haunted his September are limiting what he can do with deep routes.

3. New England’s all-star secondary hasn’t lived up to the hype.

It’s one thing to give up 300-yard passing games to future Hall of Famer Drew Brees and a reinvented Alex Smith. It’s another to allow a rookie quarterback who had completed fewer than 50 percent of his passes in the NFL look like a Pro Bowler on your home turf.

Deshaun Watson had the greatest game of his budding career against a Patriots defense that typically tears through first-year passers like tissue paper. He threw for 301 yards and a pair of touchdowns, making Sunday the third straight game in which New England has given up 300 yards or more through the air. Opposing quarterbacks have recorded a 112.9 passer rating against the Pats, the third-worst mark in the league.

That’s not what the franchise expected after adding Stephon Gilmore to a secondary that already featured All-Pros Malcolm Butler and Devin McCourty. Gilmore has been unworthy of his $70 million contract thus far, playing well on some downs and getting absolutely torched on others, like when Tyreek Hill roasted him for a 75-yard touchdown in Week 1. He’s so far behind the play he barely even shows up in this GIF:

Butler has been even worse, playing badly enough to get shifted out of the starting lineup in Week 2 and generally doing a poor job of capitalizing on 2017’s contract season. McCourty has had his share of blown coverages as well, watching each of Watson’s touchdown passes from a step behind his assignment Sunday.

“I think Bill [Belichick] said it best after the game. We’ve got a lot of work to do,” McCourty told reporters after Week 3. “It’s just a constant work in progress. We’ve got to keep after it.”

Through three games, the team has only one non-Hail Mary interception on the books. The most effective cornerback on the roster may be Jonathan Jones, a former undrafted free agent in his second season with the team. That’s not what the team expected when it locked down two premier perimeter defenders last offseason.

The good news is the Patriots have the personnel to correct these flaws.

Gillislee may not be the kind of player who can lead the league in rushing efficiency without McCoy grinding down defenses in front of him, but the young back is the kind of hard-charging runner who can thrive behind a solid blocking scheme. That’s something that should improve in the coming weeks; New England’s offensive line issues have been partially attributable to injury — Cannon and Cameron Fleming have each missed games.

While Gilmore may be an overrated piece of the puzzle, he and Butler are both above-average starters who can, at the very least, maintain a similar level of play to the 2016 unit that won a Super Bowl. That unit hasn’t been helped by a questionable pass rush. Since last year’s title win, the team has lost skilled penetrators like Rob Ninkovich, Jabaal Sheard, and Chris Long. Rookie Derek Rivers, who was expected to contribute, also lost his first season to an ACL tear.

The good news is that the pass rush is slowly developing on the backs of young linemen. Trey Flowers continues to be the team’s top pocket-collapser, and the play of rookies Deatrich Wise and Adam Butler should only improve as the season wears on. Their ability to crowd backfields and cut down passing time will be paramount to getting Gilmore, Butler, and the rest of the Patriots secondary back on track.

Any one of these flaws could be fatal to New England’s quest to repeat, but a busy offseason has ensured that the answers to the team’s biggest questions through three weeks remain on the roster. Injuries and defensive lapses have gotten the team off to a rocky start despite its 2-1 record. If Belichick and his staff can’t correct them, the franchise could be looking at a rough road through the AFC come playoff time.