One holidaymaker said she was due to fly home on Wednesday, but her hotel told her that she might be held at the airport unless she pays her bill, the BBC said in the report.
In another Cuban hotel, Thomas Cook cabin crew staff said they were effectively being "held hostage".
"There are security guards at the hotel the crew are at to prevent them from leaving. They haven't even been guaranteed rooms for tonight, so it could be a case of sleeping on the reception floor," a colleague of the staff affected told the BBC.
She urged action to get the staff home, saying "they've already been through more than enough".
Another holidaymaker, said his flight was due to depart on Wednesday, but the hotel said it would not let them get on the bus to the airport until they paid.
"They say they have wages to pay and we have been using their rooms and eating their food. It's getting very worrying now."
A UK government spokesperson said it and the Civil Aviation Authority (CAA) "were working around the clock to support all those affected".
"The government have deployed teams on the ground to support those affected, and are in contact with local authorities and hotels," they added.
The developments come after the 178-year-old British travel giant collapsed on Sunday after last-minute negotiations aimed at saving the holiday firm failed, the BBC reported.
he company had worked throughout last week to seek a compromise that would inject an additional 200 million pounds ($250 million) to the 900 million pounds it had already agreed.
On Monday, the CAA started repatriating British holidaymakers who were abroad at the time that Thomas Cook collapsed.
( With inputs from IANS )