Some have written to Communities Minister Lesley Griffiths asking for clarity on the Welsh government's shared equity loans.
They claim homeowners may have to repay bigger than expected debts because of confusion about the rules.
The Welsh government said it gives Help to Buy customers clear guidance.
Launched in Wales in January 2014, the scheme has helped 1,200 people buy their homes.
The buyer has to find a deposit of at least 5%, with the Welsh government lending 20% and a mortgage covering the rest.
Major improvements such as building a conservatory are banned, but one buyer told the BBC's Sunday Politics Wales he had to install flooring in a newly-built house to cover a bare concrete floor.
Martin Fidler Jones from Hawthorn near Pontypridd borrowed £37,000 through the Help to Buy scheme in October 2014 to help pay for his £185,000 home.
After installing the flooring, he claimed he faced a "tax" on making the house habitable, as he would have to pay back 20% of its increased value when he eventually sells it.
"I think there'll be a great number of families along the line who'll get a significant bill from this without necessarily signing up to that in the first place," he said.
A Welsh government spokesperson said there was nothing to prevent Help to Buy owners from undertaking "small DIY jobs to make their homes more comfortable".
But the spokesperson added that "significant home improvements" were not permitted, "to protect customers from making investments which would increase the value of their property and, as a result, also increase their debt to the Welsh government".
Sunday Politics Wales is on BBC One Wales at 11:00 GMT on Sunday 15 March.
People who buy houses through the a 'Help to Buy' scheme could be penalised for making basic home improvements, fear assembly members.