Khawaja and opener Joe Burns were omitted for the third and final test in Colombo, which Australia lost to slump to a 3-0 series whitewash.
Although both the Queenslanders struggled for runs, Khawaja told local media over the weekend he felt they were unfairly singled out.
“It was disappointing that Joe Burns and I were sort of the scapegoats for not performing,” Khawaja told Fairfax Media.
"I found it pretty fickle that the selectors dropped me for the third one."
Khawaja's comments came less than a week before Lehmann and selectors Rod Marsh, Mark Waugh and Trevor Hohns, pick their squad for the three-test South Africa series starting in Perth on Nov. 3.
Lehmann said he would talk to Khawaja but denied the batsman's comments would count against his hopes of a recall.
"He is not on the back foot," Lehmann told local reporters in Brisbane on Tuesday. "(But) I will chat to him privately.
"We would rather have these things played out between selectors and players."
Khawaja and Burns both enjoyed outstanding home summers against New Zealand and West Indies but struggled on the flat wickets of Sri Lanka in August where they averaged 13.75 and 8.50 runs respectively.
"Being on the selection panel for the test match, it was warranted," Lehmann said of their omission in Colombo.
"At the end of the day, there were different conditions and those two guys weren't playing well enough -- they averaged eight or seven in two test matches.
"We had to change something, but that doesn't affect the summer at home.
"We have to work out what we think the best batting line-up is for the summer."
Khawaja and Burns are hoping to impress selectors in Queensland's day-night Sheffield Shield match against New South Wales this week.
Western Australia batsman Shaun Marsh, who replaced Burns and scored a century in Colomobo, is also bidding for a top order spot as he recovers from a hamstring injury.
(Reporting by Ian Ransom; Editing by Peter Rutherford)
