This used to happen to me pretty often when I would update emacs, relaunch it, and then immediately update packages. What I saw was that async native compile would schedule/start a file, package.el would update that elpa package with new code, and then async-jit-native-compile would try to compile the since-replaced file.
It went away when I started giving the new emacs a little time to catch up before running package-list-packages; I would sometimes manually work around the problem with package-recompile-all.
I started a bug report and then stopped, because it was very closely tied to the developer-centric behavior -- I didn't see it if I let the new emacs "settle" for a few minutes of normal use.
Hope that helps,
~Chad