The Spurs have raced out to a league-best 29-6 record through the first two-plus months of the season, but coach Gregg Popovich isn’t convinced that his team should be considered great.

“We’re not going to be the Chicago Bulls of Michael Jordan’s era,” he said prior to Wednesday night’s showdown in Boston.

Popovich is concerned about a facet of the team’s game that has long been a staple of their success.

Defense.

San Antonio is allowing 103.9 points per 100 possessions (ninth in the NBA), which isn’t shockingly bad, but some of their other defensive numbers are more alarming.

Opponents are shooting 46% against the Spurs, far-and-away their worst percentage over the last decade. Just a few years ago, San Antonio held their opposition to just a touch over 40% from the field over a full 82-game slate.

“It’s something I just haven’t figured out,” Popovich said. ‘We just go through periods, like [Tuesday night in New York], when numerous people aren’t guarding anyone.”

They have allowed opponents to make 39.7% of their three-point attempts. Only the Clippers and Cavaliers, who are a combined 19-51 this season, are allowing teams to make threes at a higher rate.

Popovich added that it’s “frustrating,” because his veterans are aware of the issues.

The Spurs have excelled offensively this season, which has allowed them to overcome their defensive shortcomings. They have the league’s fourth-highest field goal percentage (47.3%) and are first overall in offensive rating (112.3 points per 100 possessions). The franchise has never had a higher ORtg.

They also rank 10th in the NBA in rebounding differential (+1.3).

Popovich is getting concerned enough about San Antonio’s defense that he’s started to implement some strange substitution patterns. He called two timeouts very early in Wednesday night’s close loss to Boston and pulled a number of his starters early on when the Celtics, largely on the strength of Ray Allen’s jumper, were hitting nearly every shot they took.

Boston shot 61.3% in their 105-103 win, including 55.6% from three-point land.

DeJuan Blair played just four minutes in the first half and the bench (George Hill, Matt Bonner, Gary Neal and Antonio McDyess) totaled 99 minutes against Boston.

Popovich’s quick trigger came just a day after he replaced his starters somewhat early in the team’s 128-115 loss to the Knicks.

He pulled Tim Duncan, Richard Jefferson, Manu Ginobili and Tony Parker with more than three minutes left in regulation and New York leading by 11 at Madison Square Garden. The 128 points were the most the team has allowed since the Tim Duncan Era began in 1997.

“I didn’t think we were going to win,” he deadpanned nearly 24 hours later.