One was cornerback Jalen Mills, who surrendered 51 yards on pass interference calls -- with one of those infractions putting the Colts on the Philadelphia 15-yard line and led to their only touchdown of the game.
The other was the offensive line, which allowed five sacks and seven hurries of quarterback Carson Wentz. It wasn't exactly an ideal situation for the Eagles' franchise player who was competing in his first game since tearing two ligaments in his left knee on Dec. 10.
Mills, who was drafted in the seventh round out of LSU in 2016, is in his second season as a full-time starter.
The two penalties were glaring, but Mills did record five solid tackles to prevent big gains and registered a pair of pass break ups.
"Jalen has actually been playing extremely well," Pederson said. "The flags [Sunday], obviously, he has to get his off hand -- he has a right or left hand going for the ball -- and the off hand is in a position where he's hooking. He has to be cognizant of that, aware of that, and try to get it off, but he's always in position. It seems like he's right there to make a play. He's physical, he's tough, he can come up and make tackles. He's been solid quite honestly."
As for the offensive line, it was a mixed bag.
They blocked well in the run game, opening holes big enough to churn out 152 yards on the ground. It's a number that may not have been expected since the Eagles were without their two top running backs in Jay Ajayi (back) and Darren Sproles (hamstring). Corey Clement also was listed as questionable going into the game with a quad injury.
Pederson, though, spread out the carries and running backs coach Duce Staley employed a liberal rotation system with the backs he had available.
It was in the pass game that the offensive line struggled, but Pederson didn't say it was solely the offensive line's fault that Wentz went down five times.
"It's really three things," Pederson said. "One, the offensive line gets beat, sack, it happens. Second one is the quarterback hanging onto the ball or tries to scramble, gets sacked, or the third one is just a flat-out coverage, they got you wired and you're trying to extend the play.
"It was a little bit of all three of those [Sunday] with the five sacks, and a couple situations where you throw the ball and skip it and not put yourself in that situation, but they're all teachable and all correctable."
Pederson said he will have more information on Wednesday regarding the knee injury sustained by safety Rodney McLeod. The coach said McLeod is still being evaluated.
Also, Ajayi and Sproles are both day-to-day, according to Pederson, although he said they could be ready to play Sunday when the Eagles visit the Tennessee Titans.