SA swimmer Shireen Sapiro was disqualified after she went to the bathroom and arrived two minutes late in the first call room.
Chef de mission Pieter Badenhorst said Sapiro made a mistake but she was fortunate in that it was not her strongest event.
"It shouldn't have happened and it's a disappointment for us," Badenhorst said.
"Fortunately, it was not her main event but still, things like that shouldn't happen."
Sapiro went to the bathroom and arrived two minutes late in the first call room. The International Paralympic Committee swimming rule 2.7.3 stipulates that all swimmers must be in the first call room 20 minutes prior to the start time of their race.
Sapiro failed to achieve this and, as a result, she was disqualified. "I've known swimmers to arrive 10 seconds late and still get disqualified," said Badenhorst.
"It is a very strict process and Shireen will learn from it.
"She was upset but it will not affect her performance and she will make sure it does not happen again."
Sapiro won a gold medal in the 100m backstroke S10 in Beijing and would be looking to defend her title on Tuesday.
The 21-year-old from Krugersdorp was a South African national junior swimmer before becoming disabled in 2004.
Her right leg was severed and her pelvic girdle shattered in a water skiing accident. She fell into the water and was unsighted by a passing boater, whose propeller sliced into her, causing the severe damage to her body. – Sapa