First of all, this is what I currently get:
error itms-90161: "Invalid Provisioning Profile. The provisioning profile included in the bundle be.x.x [Payload/x.app] is invalid. [Missing code-signing certificate]. A Distributiion Provisioning profile should be used when submitting apps to the App Store. For more information, visit the iOS Developer Portal.
I got this error message before I created the corresponging version in itunnesconnect.apple.com. After I created the correct version, I could upload my app using Application Loader 3.0.
When my new version was in status "waiting for review", I had to create a newer version. In order to do this, (according to the message I got in the website) I had to cancel the version which was waiting for review. I cancelled it and changed its version to the newer version.
And now, although the version I send and the version whose status is "prepare for submission" in the website, are the same, I still get this error. But I'm pretty sure that there is no any issue with the provisioning profile and so.
How can I solve this? Was there better way for my case (deleting waiting version and uploading instead newer version)?
Although it is not a directly answer for my question, I solved it:
I just switched from the program Application Loader to the latest version of Xcode. The problem probably comes from the way Application Loader connects to tunnesconnect.apple.com because I didn't change anything in my project and just created a new archive using Xcode and it is succeeded to upload it properly to my account.
Also: deleting waiting version and uploading instead newer version is currently the only way to do that according to the messages appeared in tunnesconnect.apple.com