"It was obviously a breakdown of communication but in these days of professional sport where you're being paid good money, you shouldn't really make that mistake," Waugh told reporters in Sydney on Wednesday.
South Africa tied their final rain-affected match against Sri Lanka on Monday in Durban to go out of the tournament.
The home side were still well-placed when heavy rain cut short the game. South Africa, on 229 for six, were one run short of the score required for victory under the Duckworth-Lewis scoring system for rain-affected run chases.
"As a captain, you get the (Duckworth-Lewis) printout at the end of the innings so you know exactly what the situation is," Waugh told reporters in Sydney.
"I think you can get it ball-by-ball, so I find it hard to believe that they had a mix-up
Pollock said after the game that 12th man Nicky Boje had been sent on the pitch to tell batsman Mark Boucher that 229 runs were enough to win. In reality, 230 were required.
Boucher hit what proved to be the penultimate ball of the match for six to take the score to 229, then defended the final delivery of the 45th over before the umpires called off the match.
Some commentators believe South Africa failed to realise that the Duckworth-Lewis over-by-over tables show what is needed to tie a game, not win it.
South Africa's team management, however, say Boje was turned back by the umpires and was not allowed to explain the full situation to vice-captain Boucher.
Waugh captained Australia to victory in the World Cup final over Pakistan in 1999, after qualifying for the final following a tied semi-final against South Africa.