Jersey Consumer Council said it heard from several parents after the incident in Jersey in which another girl was also reportedly forced to use her pocket money to pay a £50 baggage charge.
The airline says it was "very concerned" by the allegations and investigated them as a "matter of urgency".
"In the case of the 12-year-old passenger, our agents were advised her parents had left the airport confines and they failed to respond to any of the phone calls made.
"Flybe is advised by its agents that during this time, they did not immediately board the minor, however having failed to contact the parents, were not prepared to offload or cause hurt so they took the decision to nevertheless board her on to the flight together with her hand baggage which was carried in the hold free of charge," it said.
The airline apologised for the distress the girl experienced but said the agents at the airport resolved the situation in a "satisfactory and sympathetic way".
Girl, 12, 'left in tears' over Flybe £50 baggage charge
BBC Radio Jersey
A 12-year-old girl burst into tears after she was told to pay an extra £50 baggage charge on a Flybe flight from Jersey to Doncaster because her bag was too big, according to the Jersey Consumer Council.
Another young girl was reportedly forced to use her pocket money to pay the charge.
The airline has been enforcing its baggage policy more strictly since January.
Carl Walker from the Jersey Consumer Council said several parents had been in touch to complain about the way in which the charge was being enforced.
She was in tears, she was frightened, she didn't know what to do. Obviously, she couldn't appreciate what was happening - she's just a child.
Flybe said it was taking the allegations seriously and would be investigating the matter.
Back to Flybe which has confirmed its assets and operations are now owned by the Connect Airways consortium.
Flybe Group itself has not changed hands. It is
now a shell company, and the £2.8m paid by the consortium is not expected to go to
shareholders and be used for “transactional, residual and rundown costs”.
Shareholders will get to vote on Connect’s 1p a share offer on 4 March.
Heathrow link 'welcomed' by IOD and Chamber of Commerce
BBC Radio Guernsey
Guernsey's Chamber of Commerce and Institute of Directors have welcomed the announcement of a daily Heathrow service from the island.
The flights will begin on 31 March.
Both the IOD and chamber said in a statement they believed the link was cost effective and praised the move for offering a more convenient method for international travel to and from Guernsey.
They also said the move reflected feedback they have had from the business community in 2018.
The joint IOD and chamber survey in 2018 suggested respondents wanted an airline that offered a choice of domestic and international connections.
The two bodies are encouraging islanders to take advantage of the Heathrow link to make it a "permanent" selling point for the island.
BBC Radio 4
Flybe has received a takeover bid from a consortium - which includes Sir Richard Branson's Virgin Atlantic - at 1p a share. The deal has provoked some controversy.
Emily Waterworth of Brewin Dolphin told BBC Radio 4's Today Programme that she would not want to be investing in the aviation sector.
The sector has proved difficult with other airlines collapsing.
"There's clearly problems as result of the uncertainty caused by Brexit but also problems with high fuel prices and overcapacity," she said.
'Lack of transparency'
BBC Radio 4
Flybe has announced a takeover by a consortium - which consists of Sir Richard Branson's Virgin Atlantic, Stobart Group and investment firm Cyrus Capital. But there is opposition to the deal at 1p a share.
Eric Kohn, an aviation expert and chair of Barons FInancial Services, has been proposed by investors as an independent chairman.
He told BBC Radio 4's Today Programme that the takeover lacked transparency and that a bid had been tabled at a much higher price of 47p up to eight months ago.
"It appears to have a lack of transparency to it and it needs a lot of explanation. I was nominated by
one of the shareholders to become an independent chairman they still haven’t announced
the date [of the shareholder meeting] where I’d be considered and the current chairman, despite the last five year’s performance, has refused to step down”.
Flybe declined to appear on the programme, but has previously said that pressure from credit card companies made it necessary to agree the takeover.