Hello!
First, the number of valence electrons VASP considers is determined by the POTCAR files (look for the value of ZVAL). In your case, as you mentioned, there are 4 valence electrons for carbon:
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POTCAR: PAW_PBE C 08Apr2002
VRHFIN =C: s2p2
LEXCH = PE
EATOM = 147.1560 eV, 10.8157 Ry
TITEL = PAW_PBE C 08Apr2002
LULTRA = F use ultrasoft PP ?
IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no
RPACOR = 1.200 partial core radius
POMASS = 12.011; ZVAL = 4.000 mass and valenz
RCORE = 1.500 outmost cutoff radius
RWIGS = 1.630; RWIGS = 0.863 wigner-seitz radius (au A)
However, in the OUTCAR file we find this section you are referring to:
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total charge
# of ion s p d tot
------------------------------------------
1 0.876 1.750 0.000 2.626
2 0.878 1.744 0.000 2.622
3 0.885 1.775 0.000 2.660
4 0.887 1.779 0.000 2.666
5 0.881 1.747 0.000 2.628
...
I agree that the term "total charge" may be a bit misleading here. Actually, the column "tot" gives you the integrated charge density over a sphere with radius RWIGS (also listed in the POTCAR file) around each ion. The preceding columns correspond to individual contributions from projecting onto spherical harmonics. The actual formula behind these numbers is given on our Wiki here. The default sphere radius will typically leave some space in the simulation box uncovered, hence you will probably always "miss" some charge density outside the spheres. Therefore, it is expected that the individual charges and their sum in this table are typically lower than the number of valence electrons considered. See also the discussion on the RWIGS Wiki page.
Hence, although these numbers do not add up to the total charge in your system, the molecule is not charged with the "missing" charge. The discrepancy is merely expressing that electrons cannot be located and the charge cannot be "assigned" to certain ions.
All the best,
Andreas Singraber