And there are also concerns that around 40 jobs could be at risk at Forthway, which has a number of showrooms on the town's Blackwood Road.
It is thought that the company is about to go into receivership.
Steven and Natalie Falconer had traded in their three-year-old Renault Clio for £4,600 toward the cost of a new £13,000 Seat Leon.
But after the Eastfield firm hit difficulties, they are worried that they may never see either the car, or their money again.
It's a particularly bad blow as Natalie is five months pregnant and is still recovering from brain surgery.
Steven said: "We ordered the car from Forthway four, or five weeks ago and were told it would take 12 weeks to arrive.
"We're concerned about reports that Forthway has gone into receivership.
"My wife is five months pregnant and the car was our only collateral.
"I have been into Forthway and the staff are as much in the dark as we are.
"They only got told on Thursday night, or Friday morning that the company was going into receivership and they might not have a job.
"We are worried about our money, but we're also sorry for the staff there, because that's 40 people not getting paid.
"I spoke to the operations manager, Stuart McPhail and he told me it's the receiver I need to speak to.
"I'm not having a go at the staff, because last week they told me everything was okay and I think that they believed that was the case.
"As far as I know, we are the worst affected customers, because I was told that the most anyone else was owed was £1,000.
"Right now, I can't see how we are going to get that money back.
"I'm also worried about Natalie, because she's been getting worked up for the past two days and I don't know if it's damaging the baby.
"She had brain surgery last year as well and is still really recovering from that."
Forthway operates franchises for Citroen, Hyundai, Seat and Chevrolet, but also offers used cars, servicing, financing and insurance.
The company is also home to REVS, Scotland's biggest independent performance and styling accessories centre and a Peugeot scooters outlet.
Transporters are believed to have arrived and removed many of the franchised cars over the weekend.
The business, originally owned by the late Andrew Forrester, was taken over several years ago by Peter Ferguson, who is understood to live in Australia, but has returned to Glenrothes to deal with the crisis.
Town MSP Christine May said that if the company, as expected, goes into receivership, she would hope that the business could continue trading until a new buyer was found for the benefit of both staff and customers.
"It's obvious that if people have paid deposits and are waiting for a car, they're not going to known what's happening, so it's important we're given some answers soon." she added.
The Gazette contacted the company on Tuesday morning, but were told that senior staff would be in meetings all day and no one was available for comment.