The Better Government Association (BGA) determined that some of the wood planks on the platforms are deteriorating.
According to the BGA report, the Brown Line's Chicago Avenue station is the worst, with more than 80 boards that need to be repaired.
Meanwhile the CTA says it is continuing to complete the project in the interest of safety.
"I don't think anything actually went wrong," said CTA President Richard Rodriguez.
Rodriguez said that riders are safe as he explained why his cash-strapped agency was forced to spend hundreds of thousands of dollars to replace sections of the Brown Line's wooden "L" platforms only a few years after they were renovated as part of a $530 million facelift.
"There is no additional funding that's been spent - this is part of our routine regular budget that we budget and we allocate every year for maintaining and replacing things in our system," said Rodriguez.
The Chicago Avenue station is one of eight along the line where about $300,000 was spent replacing an estimated 10,000 square feet of pine decking.
"This is a good, I think, example of waste and malfunctions that happened in the project," said Patrick Rehkamp of the BGA.
Transit officials say they were alerted to the problem by rider emails and worker inspections two years after work on the first stations was completed. According to the BGA reports, a spot check found platforms with dozens of splintering wooden planks. Some even had holes and appeared to be molding.
The CTA blames the decaying planks on Flame Safe XT, a preservative applied to the wood that it said is both a fire retardant and weather sealant.
The owner of a company that makes Flame Safe XT says the product is really a fire protectorant and less a weather sealant or for long-term weather protection.
The CTA eventually had another contractor apply weather resistant preservative last year.
"This wasn't a lot of money, it was $300,000 out of a $530 million project, so it is a small fraction, but you're probably looking at four or five employees that they could have kept," said Rehkamp.
CTA officials say no injuries have been reported as a result of the decaying platforms and add that there was never any imminent danger.
"Be mindful of the fact that we have brought back over 500... closer to 600 of our laid-off employees, so we continue to bring everyone back," said Rodriguez. "It's just perception."
The BGA says it is going to continue to monitor the situation.