Well, it's a little more nuanced than that article makes it seem. The EPA’s Drinking Water State Revolving Fund is run at the state level. The "federal" part is essentially handing out the money. Miguel Del Toral is the guy inside the EPA who started raising the alarm last April. That report of his rose to the mid-regional level at the EPA where things get a little murky on how they were handled. What did come out of it is that the EPA division chief, Susan Hedman, who called his report premature later ended up resigning.

From there is appears like the EPA was in a heavy behind-the-scenes battle to get the State of Michigan to respond appropriately. Thinking of the timeline, in April Miguel writes his report. In June he gets the "premature" label, and in October everything busts wide open. It's definitely government slow level-development, but you have a lot of inter-agency communication and legal power-wrangling happening in the process. From there my knowledge gets less than ideal, but I believe the EPA can strongly encourage a course of action for the State to take (which they were doing) or force action through a prosecution by the Attorney General. In the latter case you're talking about a significant action, and one where you're getting the courts involved. That's obviously not a small decision to make. The other exception that allows them to act is the State declaring an emergency, which Governor Snider only decided to do once it became clear that Federal Investigators were looking into things.

To me it looks like the federal level lesson is that the EPA needs some more teeth to bare in cases like what is happening in Flint.