Your compiled and "generated" .swf file may have been opened in another application while Flex Builder was trying to re-compile or inject code changes back into the .swf.
If that is the case, you can solve the problem and avoid the error by closing the applications that have opened the .swf file before you switch back to Flex Builder and start coding again.
Please note that if you are developing an AIR application you should close the AIR app, or if you are working on a web application close the stand alone flash player if you are testing your app that way.
Web browsers like Firefox, Internet Explorer or Safari are an exception because they don't lock open files and Flex Builder is able to re-compile even though your application is running in the browser, of course you will need to hit refresh in your browser to see any further changes.