Helen Harker said her son Emeka was thrown off a bus
An estimated 500 parents have complained to Transport for London (TfL) about the implementation of new photo IDs for young travellers.
From June, 11 to 18-year-olds eligible for free travel must carry and validate an Oyster photocard on a reader.
Parents have complained that delays in processing the photocards have led to some children being thrown off buses and trams.
But Tfl said drivers should allow "vulnerable children" to travel.
TfL also denied there was a backlog in applications and said parents have had five months to apply.
Helen Harker's 11-year-old son Emeka has been thrown off the bus on the way to school.
"It's his first year at secondary school and you've got these people denying you access to the bus and leaving you stranded on the side of the road," she said.
Unions said the initiative had put transport workers in a difficult position.
"On the one hand drivers are being told that children must show their Oyster cards and if they don't have them to politely tell them they can't board the bus," said Peter Kavanagh from the Unite union.
"But on the other hand many of these drivers are parents themselves and don't want to leave a child in distress."
He called on Tfl to have "more consistency" when implementing new initiatives.
Steve Burton, a spokesman for Tfl, insisted bus and tram drivers should use their discretion.
"If there's a vulnerable child on the network then our drivers will take a view and allow them onto the bus."