Clandestine means kept secret or done secretively, another way of saying hidden. So a clandestine grave is one that's hidden, not one that is easily seen/marked in a graveyard. An example of a clandestine grave might be that of a homicide victim buried in the woods where no one is likely to find it.
Because the grave is hidden, geophysics (involving the use of a variety of electromagnetic techniques) can be used to outline, discover, and plan an exhumation including ground-penetrating radar (GPR), terrain conductivity (EM), thermal infrared (IR) imagery, as well as magnetometers and metal detectors.
Frequently, when the potential location of a clandestine grave is determined, the first impulse by investigators is to start digging, often with a backhoe. The result of this haste is that much of the peripheral, ancillary, but supportive evidence associated with the actual burial is destroyed, either by the excavators, or the first responders on the scene. Post-mortem damage to remains during disinterment can benefit the defense in a criminal case, jeopardizing a clear conviction. You locate the body, but end up losing the case. Get more details ForensicMag.