I have this too, and I have a theory...
If you continue using the pencil on the artboard, all is fine, but when you swap tools or click a colour swatch etc. you have to tap twice on them. When you return to the artboard to have to tap twice to get going. My theory is switching from using the artboard to using elements of the user interface requires an initial tap to switch modes before being able to continue.
It could be Illustrator that causes this issue (it doesn't appear to happen anywhere else, even in other Adobe apps like Photoshop), but I have noticed that whenever I save anything these days I have to click in the filename field to type in the name - i.e. the dialog box appear and is then unselected. So it could be something to do with a change to Apple's operating system.
Anyway, theories are all well and good, doesn't help to solve the problem. Really annoying though. Spoils an otherwise effortless drawing experience.