As the cars were being rolled out to the track, NASCAR noticed the right rear quarter panels had been manipulated around the deck lid area.
NASCAR inspectors pulled the cars out of line, and the teams corrected the issue before going back through tech.
Kenseth led the team with a third-place qualifying effort and will start Sunday's Hellmann's 500 Chase for the NASCAR Sprint Cup race (2 p.m. ET, NBCSN, MRN, SiriusXM NASCAR Radio) from the second row. Hamlin will start eighth. Busch will begin 14th. Carl Edwards, who drove the only JGR car not tagged at inspection, will start 13th.
However, Edwards' No. 19 team did lose its pit stall selection for a fourth warning related to inspections. Kenseth's team lost its pit stall selection for the same reason.
"The bodies on these cars can be pushed and prodded and these teams are very smart at the areas … for a bunch of little gains," NASCAR's Senior Vice President for Competition Scott Miller said. "It's nothing huge but it's our job to make sure it's even across the board and that's what we do. A little infraction is an infraction, right?
"The quarter panels appeared to have been messed with around the deck lid and we brought them back in and rectified it."
Busch said after qualifying that he wasn't too concerned with the situation.
"Not my problem," Busch said. "I just worry about driving and doing the best I can do there, so did everything right and we ended up exactly where we thought we were going to -- 14th -- so we'll take it. That's fine and we'll go racing tomorrow and see what happens from there."
He said his No. 18 Snickers Halloween Toyota didn't really feel any different from Friday practice to Saturday qualifying.
"Everything was really the same, you know?" Busch said. "We did some single-car stuff yesterday just barely. Didn't really do a full mock run or anything and taping it down or anything like that, but knew we had decent speed."
"... We'd love to be able to finish these things and that's all we've got to worry about tomorrow is being able to capture the right amount of points and be able to move on."