Unlike the other cases reported, there's no cracks coming from the rack, so there is possiblity of it coming from a rock chip.
When installed correctly, the rack should not touch the glass at all. Some people over tighten and have even broke the glass just during installation. There are also cases where the glass is uneven and is raised where the rack is (in which case warranty may cover). People have mentioned a piece of paper should be able to slip under the rubber part between the glass and rack.
You can always try to request warranty, but if they end up denying, note for a small crack like this a glass repair service (like that for windshields) might be able to repair (although you would need to remove rack for them to access). Some insurance policies also cover glass repair (although not always for roof).