I’m having a similar issue. sometimes the strokes will either “stick” to the pixel grid and either appear invisible or/and off-cursor until i release the left click and downright “ignore” some pixels.
Keep in mind I only released the left mouse click between shapes. as you can see, sometimes the cursor won’t fill certain areas it passes through, sometimes twice.
I’m using a Logitech MX mouse too on the latest macOS, so it might indeed have something to do with that.
Anyway it looks like the window is losing the focus, is a third-party extension/driver handling the logitech mx input? (like a software to customize their buttons etc.)
This happens to me every time I use Aseprite, but I have no mouse or drivers that would cause it, and resetting preferences didn’t work. Now I have a borderline unusable aseprite with none of my settings and windows.