Tom Brady continued his top-flight play from the Ravens game and was in complete control once the Patriots got down to basics in the second half.

The running game erupted thanks to equal parts vision and patience from rookie Brandon Bolden, play calling from offensive coordinator Josh McDaniels, adjustments at the line by Brady, and very good execution by the offensive line against a smaller Bills defense.

And on defense, the line played soundly and the linebackers made impact plays.

But if there’s one lingering concern as the Patriots welcome the Broncos and Peyton Manning to town Sunday and set course for the rest of the season, it has to be the secondary, namely the play at safety.

There was some good in there with cornerback Devin McCourty’s two interceptions, safety Tavon Wilson’s gift-wrapped pick from Bills quarterback Ryan Fitzpatrick, and all-around solid play from No. 2 cornerback Kyle Arrington.

Besides that, the Patriots internally have to be doubling up efforts to get things corrected in the secondary because the sub packages on defense are ripe for exposure by the right quarterback and team.

It can’t be sitting well with coach Bill Belichick that his defense, despite having more talent and time in the system for some players this season, is still giving up way too many explosive plays: seven of more than 20 yards (accounting for 56 percent of Buffalo’s 438 yards), and another nine for more than 10 yards.

A sampling of the miscues after watching the coaches’ tape:

McCourty actually appeared to be out of position on his second-quarter interception. The Patriots looked to be in Cover 3, with the safety and two corners responsible for a deep third of the field. McCourty let receiver T.J. Graham run by him. McCourty was lucky Chandler Jones knocked Fitzpatrick down to contribute to an underthrow.

Jones and Jermaine Cunningham kept safety Steve Gregory from getting burned on third and 12 in the second quarter by forcing an overthrow from Fitzpatrick.

On the 14-yard third-and-10 conversion to Brad Smith right before halftime, the Patriots were in a three-deep coverage with Wilson in middle of the field specificially to take that play away. Wilson failed to drive properly on the ball.

Not sure what defense the Patriots had on when the Bills converted a third and 15 on a 16-yard screen pass to Fred Jackson early in the third quarter. No one had Jackson, and Wilson appeared out of position in the zone.

Just poor safety play on the 86-yard touchdown to Donald Jones. Patrick Chung took a bad angle and missed a tackle for at least another 55 yards, then Gregory failed to hold up Jones down the field.

On the 22-yard pass to Jones in the third quarter, Sterling Moore was likely supposed to pass his man onto the safety and then sink on Jones. Moore never turned around on an easy reception.

On third and 17 late in the third, Fitzpatrick overthrew a wide-open Stevie Johnson, who had beaten Moore.

The Patriots avoided another big play late when Johnson stepped out of bounds at the 7-yard line on first down at the New England 37. The Patriots were in quarters coverage (four players split the field in quarters) and Moore sunk in the out pattern underneath, which he is likely supposed to do. Chung got caught flat-footed and didn’t pick up Johnson’s sideline vertical route properly.

The Bills’ final touchdown, a 35-yarder to Smith on third and 8, was part good play by the Bills, part bad play by the Patriots. New England was running a newer coverage, an inverted Cover 3, if you will. The Patriots show Cover 2 (two deep safeties) at the start, but at the snap, the two safeties come up to play the intermediate routes, and Wilson retreats to patrol the middle of the field. The two edge cornerbacks play over the top to divide the field into thirds with Wilson. The Bills hit the seam perfectly, but Wilson likely is supposed to recognize the vertical threat sooner.

The Patriots got away with that stuff — and more — against the Bills thanks to an offensive explosion and Buffalo’s lack of precision and ball security, but it has to be cleaned up.

The rest of the team feels like it’s ready to explode. Will the secondary catch up?

Here are the positional ratings against the Bills:

Quarterback (Rating: 4.5 out of 5)