Just a few observations:
* Work on the Grandview Triangle almost certainly required, at most, an EA. This is because the freeways intersecting at the Triangle are all established corridors and are not being widened over substantial distances with consequent impacts to traffic and hydrology, so improving the interchange is not considered a "major action" requiring an EIS. EAs are very common for urban freeway widenings and interchange improvements (the Katy Freeway in Houston was a bit of an exception since it went forward under an EIS).
* The permitting agency most directly involved in drainage matters is the USACE and it typically takes an interest only if discharges into jurisdictional waters are greater than those allowed in the permit. The problems with the Grandview Triangle are unlikely to lead to permit noncompliance because the amount of water that reaches jurisdictional waterways is related to rainfall and is ultimately the same--the problem is that, at a specific location, MoDOT clearly did not make adequate arrangements to keep it away from embankment fill.
Frankly, I doubt USACE will do anything more than ask for assurances from MoDOT that permit conditions will still be met.