The Big Forehead bug #3493
Steps To Reproduce
I've been experiencing the same issue with SizeUp (http://www.irradiatedsoftware.com/sizeup/), which leads me to think it's probably a problem with any window manager that programatically resizes the window. The two most common cases I run into are making the window full-screen, and moving a full screen window to a screen of a different size (most noticeable when it's larger, but smaller is also bad).
I never saw any issue like this on the release version, but ever since switching to Mojave, I've had the same problem on every nightly build I've tried.