Get rid of some extra resistance in your filament path by getting rid of that stupid little piece of Teflon tube inside the filament sensor cover! HOW? EASY! With the snazzy new Carbonbased Prusa i3 MK3 MMU 2.0 Filament Sensor Cover for Pass-through Couplings Thingamabober.
Simply print out my replacement cover, screw in any passthrough tube fitting with a 10mm x 0.75 thread, remove the old cover and little crappy piece of tubing, attach my cover, CUT A FUNNEL SHAPE INTO THE END OF THE ORANGE TUBE JUST LIKE THE LITTLE WHITE TUBE IF IT IS NOT ALREADY LIKE THAT FROM THE FACTORY, and push it through until it is seated. You may want to keep the two cover screws loose to allow things to line up while inserting the tube.
I also added a cable tie from the MMU2 kit around the coupling as pictured to prevent the tube from wanting to cock at a weird angle since the tube is short and gets tugged around left and right as the printer works. It may not be necessary.
You will probably have to recalibrate for the new length of the tube to the extruder (instructions in your manual) or else the mmu2 will be smashing the filament into your extruder gears.
I would also like to say that this is not my idea - I learned it from watching a troubleshooting video made by one of the beta testers:
Link to the couplings on Amazon (US):
Also, good luck getting the glitchy MMU2 to work properly.