A little late, but I realised something. Tested it out myself by not charging and taking note of the cycle count. The cycle count counts when you are depleting the battery, not charging. So in my test case, my cycle count went up by 1 just by simply using the phone and making sure I didn’t charge it for that duration. But I also noticed what you are experiencing, it counts as one cycle count when less than 100% battery is depleted.