Trott made a shock departure from the Ashes tour earlier this week after the England and Wales Cricket Board (ECB) revealed that he was suffering from a stress-related illness.
Australia's Warner has attracted criticism for comments he made during the first Brisbane Test in which he described Trott as "poor and weak".
Trott had a difficult time playing tearaway Australia speedster Mitchell Johnson and was dismissed for 10 and nine in the first Test.
Waugh, who was regarded as a hard-bitten and competitive Test captain, was critical of Warner's comments made at a post-stumps media conference during the Brisbane Test, which Australia won by 381 runs.
"He can make a generic comment, but I think when you get personal like that, you cross the line on how players treat each other, and the respect they should have.
"So I didn't agree with Dave's comments, having said that, he probably did smell a bit of fear in the England opposition players.
"Unfortunately for Jonathan Trott, it was a personal issue, and you don't want to keep going on about that.
Waugh added that Australia probably needed to be a little cleverer in how they went about things.
"They're playing well, so they don't need to do so much talking out there now," he said.
The Ashes series resumes in the second Test, beginning in Adelaide next Thursday.
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