They say here below, with 3 references, that the small moon is known to have “significant porosity” (has internal crevices). I guess that would explain the low over all density.
“Spectroscopically it appears to be similar to the D-type asteroids,[10] and is apparently of composition similar to carbonaceous chondrite material.[11] Phobos’s density is too low to be solid rock, and it is known to have significant porosity.[12][13][14]”
http://en.wikipedia.org/wiki/Phobos_%28moon%29#Physical_characteristics
Porosity would suggest a formation (perhaps from a larger former body) with high heat, resulting in expansion of various materials such as water into vapor, leaving voids as the vapor eventually escaped. On Earth we see pumice, which would be analogous, but which has the gases still in the voids. One of the problems with excavating Herculanaeum is that the stone has billions of pores still containing the poisonous gases belched up by the 79 AD eruption.