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When you have a ruby sight stone in your inventory, a lot of the time it doesn't refill when you return to the fountain. IIRC, the tool-tip states that it will refill every time you return to the shop, but it seems pretty random when it actually does replenish the wards. I've tried opening the shop, buying items, and recalling with no luck at times. Also, it seems to happen particularly during late game when all my item slots are filled. Not sure if this is a coincidence or not.
Maybe the tool-tip just needs to be updated cause i cant figure it out. Seems to do it randomly.