This is probably a topic better placed in the JLCPCB Category. Without sight of your project and files uploaded to JLCPCB it is difficult to say what may have happened. Did you set Add to BoM = Yes for all parts in the schematic? Did you generate the BoM from the schematic? Did you select all parts from the JLCPCB Assemble library? Did you check that all parts where selected for fitting in the BoM uploaded to JLCPCB? Did you check that all parts were in stock at JLCPCB?