I had the same issue.
My problem was that by renaming target, I ended up with the same Product Name for the Main app and the Watchkit App, resulting in overriding themselves while building.
So everytime I cleaned the build, on the first install it was actually working, but on the second one I was alwas getting this Error.
When I realized the problem, I also found out that Renaming the product name of the WatchKit App wasnt fixing the issue because XCode doesnt really update all the references to the WatchKit Extension target, maybe there will be a fix later for this. (At the moment i am using XCode 6.3.1)
Renaming the Product Name of the main app to a different name, fixed anyways the problem.
Afterwards cleaned and rebuilt and never had that problem again.