Started hearing a faint click at 3 o'clock on the right pedal last year early spring, got worse in the summer. No other issues just annoying. I tightened every bold I could find, tried different shoes, different SPD cleats, even regular shoes. Still, a faint click - click - click. Took it to the LBS, no issues found. Tried lubing the pedals and ruined one so I replaced with a new set, same clicks. Got fed up and decided I'd take it to a different shop so I dug up my old hybrid to ride in the meantime as this LBS had about a 1 week lead time. Aired the tires, lubed the chain, took 'er for a test ride and guess what? Click-click-click.
After taking a good look at my feet I finally mimicked the rotation motion exact enough and got a click-click-click. My FOOT was clicking, some bone or tendon was snapping. Oh, and it got louder in the summer because I switched to open toed sandals for coolness. Hence the increase in sound. I have a little bit or neuropathy in my feet so I didn't feel it, only hear it.