The Lions levelled the three-match series at 1-1 on Saturday with a 24-21 victory over the All Blacks in a match punctuated by outbreaks of pushing and shoving in Wellington, setting up a winner-take-all third test in Auckland next week.
The All Blacks had Sonny Bill Williams sent off for a shoulder charge on Anthony Watson in the 25th minute while Lions prop Mako Vunipola was given a yellow after he drove his shoulder into Beauden Barrett's head in the second half.
Lions flanker Sean O'Brien has also been cited for an alleged "swinging arm" on Waisake Naholo after the citing commissioner deemed it to be a "red card offence".
The Lions conceded 13 penalties to the All Blacks' eight at Wellington Regional Stadium as the visitors fell foul of referee Jerome Garces time and time again. Barrett slotted seven of his 10 penalty attempts.
The Lions also lost the penalty count 11-7 in the 30-15 first test loss, with O'Brien responsible for three of them.
"We can't be giving penalties away like we are at the moment," Rowntree told reporters. "We have to sort it out because it's going to kill us.
"We can't lose the test series on the back of stupid penalties. How do you live the rest of your life with that?"
Despite being a man down, the All Blacks dominated the third quarter of the match, with Barrett breaking the 9-9 halftime deadlock with three successful kicks.
Vunipola was penalised four times, as well as spending 10 minutes on the sidelines, while lock Maro Itoje and O'Brien were each penalised twice.
"There is a trait to what we're doing," Rowntree said. "In the heat of the battle under fatigue it's all about what you do and we can't be doing that."
The former England prop added that while he had not initially identified any serial offenders, if necessary head coach Gatland would not be averse to using the 'big stick' to hammer the message home or to drop players.
"I think Gats has shown he's not afraid to do things like that. But as I said it's not the same offenders," Rowntree said.
"The coaches will sit down and have a look at it and be very frank and show the lads. That will be a big focus this week."
(Editing by Peter Rutherford)
