Good news. In the latest watch os beta release notes, I found this tidbit:
When a WatchKit app is in an active debug session and in the background, you can send background tasks to the app through the Debug menu. “Simulate Background Refresh” sends a WKApplicationRefreshBackgroundTask and “Simulate UI Snapshot” sends a WKSnapshotRefreshBackgroundTask. Note that these tasks do not have any userInfo data that may have been registered from a previous request from the app. Also note that these tasks are not sent if the app is in the foreground.
Were you able to find a solution to this issue? I am still noticing this issue.