I believe this is a bug in Safari.
Safari MV3 supports the background.page key (so-called 'Event Pages') which you might be able to use as a workaround. Try something like
In manifest: background: {page: background.html}
In background.html: <script src="my_service_worker.js"></script>
Since incorporating my "service worker" like this I have stopped seeing the error (touch wood).
simplicio
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You need to turn on the debug menu in Safari
grant full disk access to Terminal
run defaults write com.apple.Safari IncludeInternalDebugMenu -bool true
In the debug menu select Extensions > reset web extensions state
But I would like to know how to do this on iOS.