Seen this mentioned in other posts but is causing a real problem for me.
I have just moved from V5 (where I did not have this issue) to V6 where issue happens all the time.
Basically the deploy process works and the code.js is uploaded to server. However the app does not update properly unless the browser cache (windows and android) is cleared manually. As I said this did not seem to be an issue in V5 where IIRC the JS was not in a separate file.
APart from adding confusion to the compile/debug cycle, it is also likely to be an end user issue as it is not realistic for many end users to either understand why or be able to clear browser cache manually.
V5 seemed to be rock solid in this respect with no caching issues noticed.