I remember one time flying SJC-SAN, I checked my bags at the ticket counter 33 minutes prior to departure (according to the time stamp on the bag tags, so it was not considered a late check-in). One bag made it on the flight, and the other came in on the next flight 1 hour later. I couldn't help wondering if some baggage handler did that just to deliberately tick me off. At check-in, I saw that the bags went onto the belt sequentially. I suppose it's possible they just forgot to load a cart, or something.