Hallo Jun,
indeed running Sen2Cor from command line without specifying any spatial resolution results in processing all spatial resolutions and thus all bands . The bands you are missing are exactly the 60m bands except band 8. I am not sure what settings are used from interface and I have no time for checking at the moment, but I assume you are processing at 20 m spatial resolution. Then bands 2-4 are resampled to 20 m, band 8 is not processed but band 8a and the 60m bands are also not processed. Note, that band 10 will be never provided with the L2A-product because you don’t the surface at this band (except over high mountains).
Your other problem (small constant values for reflectance at band 3) is probably related to overcorrection the atmospheric contribution. Atmospheric correction provides negative reflectances which are replaced by Sen2Cor by a constant, small positive value. Unfortunatley I cannot provide you a workaround for this.
bdpg