Likely CF related. Our bodies tend to be achy because of things like inflammation, coughing and fatigue from that, possible nutrition problems, mental issues (stress etc.) etc.
Stretching is great but depending on how intensely your stretching sessions are the tissue that you stretched could need time to recover and signals that it's achy the next day. Then you could do lighter days in between or simply acknowledge that it's from the stretching and keep doing that since that's not likely a bad thing then.
As usual I'd also like to recommend lifting weights..since that helps with everything and certainly gets rid of tightness and pains from coughing and all of that.