It was a disappointing loss to the Colts on Saturday night, as the Patriots looked rusty coming out of the bye week with many of the issues that haunted them earlier in the season popping back up and playing a significant role in the defeat.

Turnovers, penalties and a lack of clutch down the stretch highlighted the shortcomings, with a run defense thought to have fixed their issues getting run over by one of the best rushing attacks in the league. The Colts did to the Patriots what the Patriots usually do to most of their opponents; they won the line of scrimmage, made fewer mistakes and then just enough plays to seal their victory.

But it's not the end for the Patriots. Far from it. Maybe the top-seed bye might've slipped from their grasp without significant help, but the division title and playoffs are still very much within reach.

Here are the issues for the Patriots to get fixed if they're to put things back together and finish the season with their best football.

Penalties

The Patriots tied a season-high for penalties against the Colts with eight, with many of them coming at key points and directly costing the team points.

• Jonnu Smith had a false start on 2nd-and-1 from the Colts' 13, Mac Jones would throw an interception two plays later.
• Brandon King had an offsides penalty on a missed field goal that would result in a made re-kick.
• Jakobi Meyers had a holding call followed by an Isaiah Wynn false start that would back New England up to a 1st-and-23 from the Colts' 25, two penalties that the offense would overcome with Jones finding Hunter Henry for the first touchdown of the game.
• Michael Onwenu's false start turned a 3rd-and-2 from the Indy two-yard-line into a 3rd-and-7 that would not be converted, forcing the Pats to settle for a field goal.

A season after having a league-low 62 penalties, the Patriots are still in the lower half of the league as far as accepted penalties, but this is the third time in 2021 they've had eight accepted penalties and those games account for three of the team's five losses. It was a season-high for the offense, who took seven of the eight calls.

It's disappointing to see such sloppy play so late in the season and against the Colts, one of the least penalized teams in the league this year, the miscues were too much to overcome. Cleaning things up will be a big key in the final three games, especially inside the red zone when they're knocking on the door for points.

Run Defense

This loss to the Colts resembled 2019's playoff defeat at the hands of the Titans a little too closely. In that game, the Titans only had to complete eight passes for 72 yards while Derrick Henry ran for 182 yards on 34 carries. Jonathan Taylor had a similar type of performance, as the Colts had so much rushing success on early downs and 4th-and-shorts that nothing else really mattered.

By the time Taylor sealed the win with his 67-yard touchdown, it was the culmination of a dominant ground effort that the Patriots had no answer for. Now, Ja'Whaun Bentley's injury early in the game certainly didn't help matters, he's a key presence in the middle against the run and his toughness and anticipation were missed.

During New England's win streak they held opponents under 100 yards in five of the seven wins, but the 270 yards allowed to the Titans on the ground two games ago, and now the 226 to the Colts are concerning. The Patriots run defense was ranked dead last in DVOA last season and they took major strides to address it this offseason but against the best back in the league there didn't look like much had changed.

That said, the rushing attack gauntlet is over, at least for the rest of the regular season. A playoff rematch with the Colts, or perhaps a Derrick Henry-infused Titans, could be causes for concern but for now, the run defense can catch their breath and focus on the pass-happy Bills.

Clutch Defense

Another element of the early season struggles that suddenly popped back up was the defense's inability to play complementary football on the final possessions to give the offense one last crack. It wasn't a total disaster, with Jamie Collins and Devin McCourty combining to pick off a key pass to give the offense an extra fourth-quarter chance.

But after New England closed the score to 20-10, the defense gave up two first downs and allowed the Colts to bleed five minutes off the clock. The offense would get the ball back and close to within three points but two plays later Taylor would rip off his long run and close things out. That was two drives where a three-and-out by the defense gives the Patriots a chance to win the game.

The defense had shown some great clutch during their win streak, but it was missing against the Colts and they were never able to give the ball back to the offense when they were down by one score or less. As is always the case late in the season and especially in the playoffs, they'll need to get their clutch back.

Offensive Finish

The Patriots quickly found themselves in a 17-0 hole against the Colts and that can quickly take a team out of their gameplan. Add in the absence of Damien Harris and then the injuries that added up over the course of the game and there were some issues for them to work through while trying to come back.

The red zone has been a huge area to highlight this season, as it's been a consistent struggle with the offense landing at 26th in the league entering the contest.

They did score two red-zone touchdowns, but came up empty in the other two possessions inside the 20-yard-line, with penalties playing a part, as mentioned earlier. It's not hard to see how different the game could've been with just one more touchdown, if the Patriots were to click at a rate closer to 75 percent as desired, rather than just over 50 percent.

Plenty of fingers get pointed all around after a loss in the NFL, but there's no bigger culprit for the Patriots offensive struggles than their lack of touchdown finish close to the end zone.

Injury Issues

There are some big injury questions coming out of the loss, with Ja'Whaun Bentley and Nelson Agholor topping the list of Patriots who left the game and did not return. Both players are heavily relied upon with their roles, roles that are critical on both sides of the ball.

N'Keal Harry and Carl Davis also were dinged up in the game and while neither play the kind of roles that Bentley and Agholor do, they both have significant jobs. Prolonged absences for either could have an impact on New England's game-planning ability.

Then there's Damien Harris, who missed his second game of the season. His change of pace could've helped the Pats have more success, especially in short-yardage situations.

Late in the season, the injuries are starting to pile up. The team gets an extra day of rest and prep this week, they're going to need it with a huge divisional rematch coming up against the Bills. Getting healthy over the final three weeks before the playoffs is a big key.