I am struggling with debugging my WatchKit Extension/App on a real Apple Watch. Debugging both the iPhone App and the WatchKit Extension using the simulator the simulator is
I am having the same kind of issue but to improve a little bit the debugging experience I usually restart my devices a few times. Try to restart your Apple Watch or your iPhone.
Before launching your app from Xcode, make sure that the app is completely closed on your Apple Watch (not stuck in the loading screen for example). To do that, you have to force close the app: enter your app, keep the side button pressed until the menu to turn off the watch appears, then press the same side button for a few more seconds until the watch will go back to the homescreen and force close your app.
Now you can try to build and run the app from Xcode and it should work more reliably.
watchOS 3+:
The force quit is done by pressing and holding the side button (the button just below the Digital Crown) until the shutdown screen appears, and then let go of the side button, then press and hold the Digital Crown.