It all depends upon your machine, the application under test, and the way you are resolving the item in scripts.
You will always get that prompt, but if the item already exists, it should not remain for long. Your project has a default auto-time out setting (I think it defaults to 10000 milliseconds) so, at most, it will wait 10 seconds for the object to resolve and then it will generate an "object not found" error.
Do you have an example of a function or procedure that you are executing that is giving this behaviour? There may be some tweaks that can be done to speed things up a bit for you.
