Faulty travel smartcards have resulted in some children not being allowed on buses, making them late for school or leaving them to walk home alone.
Under-16s who are eligible for free travel need a photo Oyster Zip Card which must be validated on a reader.
But at least 29,000 of the cards failed and had to be replaced, Transport for London (TfL) said.
A TfL spokesman said of those replaced, more than half had shown evidence of misuse such as exposure of the chip.
About 500,000 Oyster Zip Cards have been issued to children in London.
Ruth Lyons, 13, said she had been told to get off buses twice because her card failed. Both times she was late for school.
"You get on a bus and automatically assume it is going to work, so you don't take any money or have a back-up plan," she said.
"And then when the reader goes red [indicating the card has not worked] you normally get kicked off the bus."
Jeroen Weimar, from TfL, said: "We ask the bus drivers to use their judgement.
"If the child is vulnerable and clearly needs to make that journey they will be carried and we have ways of getting compensation for that."
London Assembly Green Party member Jenny Jones said: "Despite the advice to drivers to use their discretion, many children are still being stopped from getting on the bus and are left to walk home on their own or being late for school.
"I think it is important that drivers are made aware of the scale of the card failures and don't punish the children for what is a problem with the system."
TfL said that since 1 October 2007, 29,000 failed Oyster photocards had been replaced free of charge.
It added that of those cards, over half had shown evidence of misuse including cracking or exposure of the chip or aerial in the card.