Had my 21' Cal on boat stands all winter. Moved 'em around a bit to paint the bottom. Same thing as you. I was dismayed to see indentation of about 1/2-3/4" at pads. Moved stands, and within a day, back to normal. Boat has a solid fiberglass hull. I had to lower my swing keel to work on it during this time, if I'd kept it retracted and supported underneath, I think that it would not have indented as much. The ideal way to support the boat is with blocking under the keel to take the weight, with the boat stands stabilizing.
I wouldn't worry unless I saw crazing of the gel-coat or glas.
“Scientists are people who build the Brooklyn Bridge and then buy it.”
Wm. F. Buckley, Jr.