Yeah, with a .4mm nozzle that sounds like something is really wrong. With a .4mm nozzle you should get a free extrusion width of about 0.48mm which should give optimal layers at 0.25mm ( https://nathan7.eu/stuff/RepRapCalculator/RepRapCalculator.html#PrintSetup )
You want a width over height ratio of at least 2.0 for strength, but more than 3.0 will start to decrease detail in the prints.
Though your Z axis mechanics will play into optimizing that layer height as well: http://www.prusaprinters.org/calculator/#optimallayer
One of the best writeups I’ve seen about calibrating extrusion is here:
I started using the same method just before she posted those and finally got things dialed in to where I could do print in place designs in any material successfully. Now anytime I get a new roll of filament I setup a new profile for it in slicer and do a couple of quick single wall test prints to dial it in. Accuracy on my prints has been great since I started doing that.