You might be referring to a few things...

If it's a black mark / bump or bubble on the inside of the shell, which is not removable, it is known as a mud blister. This is a defensive barrier against the parasite (Polydora ciliata) which attempts to bore into the oyster shell.

If it's black gunk that is removeable, it could just be mud from the exterior (as a result of sloppy shucking) or it could also be pseudofeces from the oyster itself.

Reference: http://portal.ncdenr.org/web/mf/oyster-mud-blisters