This looks like you have a problem with general stain or just plain old dichroic fog. It's not present along the edges probably due to the geometry of the tank/film holder.
To prevent this, use an acidic stop bath. You can also use an acidic fixer. This is the easiest solution, and rest assured, it will leave the stain alone just fine. The "acid stop/fix will damage the stain" is a very persistent myth - and an unfortunate one, because it can result in trouble as you've presently shown.
https://tinker.koraks.nl/photography/to-stain-or-not-to-stain-acid-and-pyro-developers/
Feel free to use a pH neutral or alkaline fixer if you want, but when doing so (esp. an alkaline fixer) it's crucial that you prevent any developer carryover into the fixer bath. A single water stop is courting disaster (as you've aptly demonstrated). If you insist on a pH neutral to alkaline process throughout, perform a couple of water rinses between develop and fix, not just a single water 'stop'.
The fact that you used EMA is likely not really a factor here, although during the long period of development, you will get a high degree of oxidization of the pyrocatechol, which may make matters worse. In general it does result in a higher base stain. This will generally not be a major issue when scanning or enlarging your film; it's inconvenient or even cumbersome when using UV-based contact printing processes.