Yes. This is common, and especially important for energy work--

More specifically, you have broken a conceptualization of what you were doing, so that it may be approached differently-- All instruction comes with baggage in the language--

However, the background thoughts are still occurring.. Just like your new approach changed the definition of experience; so to, are you still unconsciously noticing these thoughts in your "feelings"--

thoughts and feelings are not really different-- You were focusing on your conception of breath, but now you are focusing on the breathing itself-- However, even that is conceptualization of what you are doing, and as such can be broken down further--