Getting worse quality prints on 0.05 mm than on 0.10 mm layer height on Prusa i3 MK3
When printing at small layer heights (high resolution), you probably need to do some test prints first to see if your normal settings work for the lower layer height. You are most probably experiencing an increased pressure build-up in the nozzle due to the nozzle being closer to the bed. A test that might be useful for you is spacing several objects at different distances to see if the retraction, which you already suspect, may be not working optimally or that the nozzle leaks/oozes an excess amount of filament due to pressure build-up. This shows an example of such a test where the nozzle shows oozing.



Tuning the extruder to alleviate the pressure could be:


an increased retraction length, and/or 
retraction speed, or 
looking into the option called coasting where you stop extruding before the printer reaches the end of the deposition path while it still prints material caused by the pressure build-up.






When printing at 0.05 mm on my home-build CoreXY I experience much smoother prints opposed to printing in higher layer heights (less resolution), but I also get some very fine stringing, noticeable when printing multiple objects or objects with voids.