Mark Twain is supposed to have once said that there are lies, damned lies, and statistics. You have to be skeptical when a statistic like the one in question here is trotted out to create angst among the general public because no background or context if offered to help evaluate the statistic's significance. That often means that the statistic is misleading in some significant way and just for show.
Let's consider a few things. FRA inspectors are paid to find "issues," so they will find them. An inspector who finds none will probably have his employee file tagged for special attention on the suspicion he is spending his time at Dunkin Donuts or, worse, is on the take. Has Metro North been singled out by the FRA for special attention? This could easily inflate the number of "issues" found. How many of the "issues" or "defects" were things like a malfunctioning chewing gum machine at one of the stations or a non-approved design of an employee-use toilet seat at another (the latter from my personal experience with CalOSHA in a non-railroad context a few decades ago)? Nothing is easier than to find failures to comply with hyper-detailed bureaucratic regulations, or beneficial to the circulation of a newspaper or magazine like paranoia. That is what this statistic is designed to crank up.
Railroads are works of Man and so cannot be perfect. Still, I think it's safe to say that Metro North has some kind of maintenance problem, but the FRA is not tripping, so we have to presume that FRA and Metro North have, or are getting, a handle on it. If we assume otherwise we have to ask why we have an FRA to start with. If Metro North is being allowed to operate with material defects that affect safety then the problem is with the FRA, not Metro North, IMHO.
Bernie