Unfortunately, it is most likely a problem with the default ATC and/or AI Aircraft. They are...not very bright. We are working on some bug fixes that we hope will make it much better to use, but they are not out yet. I know that is not very helpful, and this next suggestion isn't very realistic, but the only thing that you can really do at the moment to make ATC better for your flight would be to turn off or reduce the AI aircraft so they can't get in the way.