An MTA upgrade to bring a subway station into line with the Americans with Disabilities Act had to be redesigned in the middle of construction — at a cost of $617,000 — because the agency somehow forgot to make the platform wheelchair-accessible, according to a new report.

It was just one of many costly blunders in the agency’s design and construction process that delayed six New York City Transit capital projects in recent years — causing them to run over budget by a combined $42.3 million, an audit released Monday by State Comptroller Tom DiNapoli found.

Other budget-blowing problems included transit officials’ slow response time to contractors’ questions, a lack of independent review for pricey project changes requested by contractors, and shoddy oversight of contractor staffing levels, his office found.

“This audit found numerous problems in the MTA’s capital projects pipeline that led to delays and cost overruns,” DiNapoli said in a statement. “These are red flags that fall within the MTA’s power to fix.”

The wheelchair bungle happened on the MTA’s $21.7 million accessibility overhaul of the 23rd Street and Lexington Avenue station, which wrapped up in December 2016 — ultimately $3.2 million over budget and 27 months behind schedule, according to DiNapoli’s office.

The design was supposed to bring the hub into compliance with federal disability laws — but it didn’t raise the platform edge for straphangers in wheelchairs, and the agency only realized mid-job, the audit says.

On another project — a $389 million effort to overhaul signals on the 7 train — a contractor was supposed to have a “quality assurance” staffer on hand, but auditors found “no evidence” such a person existed.

It finally finished earlier this year — $15.5 million over budget and 21 months behind schedule.

Meanwhile, a contractor performing a $237 million signal project on the 5 line in the Bronx paid employees for 378 total days of work between January and March 2014 — even though the workers were only present at the project site for about half of that time, the audit found.

The six projects are all part of the MTA’s $33 billion 2014 to 2019 capital plan. The next capital plan, set to be released later this year, is expected to cost well over $40 billion.

In a written response tacked onto the audit, subways chief Andy Byford claimed the report “infers cause and effect without a rigorous evaluation of schedule and budget” — and noted that “the combined costs of design errors and omissions for the six projects represent .35 percent of their total budgets.”

The British-born railway exec said contractors determine their own staffing levels, and are held accountable for any delays or cost overruns.

In a statement Monday, MTA spokesperson Shams Tarek claimed DiNapoli “cherry-picked” six of the agency’s more than 2,000 recent capital projects.

“The auditors themselves note that their samples were not designed to be representative,” Tarek said. “While we don’t agree with most of the auditors’ findings, the MTA is taking aggressive actions to hold contractors more accountable.”

But transit advocates say DiNapoli’s report barely scratched the surface of the MTA’s ballooning construction costs, which extend far beyond the subway system.

“It’s helpful to see some of these sources of delay, and the recommendations about day-to-day project management are worth considering, but they left out a lot of the big cost drivers,” said Ben Fried of Manhattan-based think tank TransitCenter. “This report… aims too low to really drive change.”