Using a Positronium as my example.
the mass of 1 electron is 9.10938291(40)×10−31 kg
the mass of 1 positron is 9.10938291(40)×10−31 kg
The two particles annihilate each other to produce two gamma ray photons after an average lifetime of 142 ns in vacuum.
leaving behind 2 photons, whose mass is so near 0 we say they have <1×10−18 eV
1 MeV: is about twice the rest mass-energy of an electron.
hence what is produced does not equal what we started with, 1+1 is not equaling 2, so where does the mass go?
The mass of a photon is not "near 0", it is 0. Photons are massless. The contribution to mass comes from the energy of a photon, this follows e=mc2.