Yet another client-side check?
It makes sense that a client should such checks rather than the NRS itself - the server side is correct to assume "that you know what you are doing" so if you ask to re-assign an alias to the same value then as far as the server is concerned that is what you meant.
The other way I guess it could be resolved would be to have a "second parameter" to the alias API that states whether it is "creating" or "updating" the alias.
The client displayed me an error about a timeout. I didn't tought it went trough. But after it billed me for both aliases (same alias, same URL). I'm not sure if I understand you correctly: This is only a client problem and the two same aliases I get displayed under "Account aliases" are a bug? I not got the same alias twice, but I payed for the same alias and URI a second time (for the assignement). Right?