NASA's acting administrator Robert Lightfoot told the WSJ that government officials have known about the issue for months or even years. The agency even told SpaceX that the cracks are too much risk for manned flights. However, the congressional watchdog will still write about the issue in the final report it's slated to publish in the next few weeks because the company found cracks in their turboblades as recently as September 2016.
A spokesperson said SpaceX has "qualified [its] engines to be robust" to cracks, but it's now "modifying the design to avoid them altogether." The company has been working with NASA to fix the problem, though they're unsure if it would require a complete redesign. If it does, it'll likely take a lot of time, which will, in turn, push back the company's launch schedule.
In fact, GAO has already determined that both companies will likely miss their goal to start ferrying astronauts to the ISS in 2018. Besides this particular problem, the investigators cite Falcon 9's frequent modifications for the delay. In Boeing's case, the investigators have raised concerns about the status of the tests designed to determine if its manned capsules' landing parachutes are reliable.