I am not a historian, however, I am a physician and feel I can answer this within the guidelines of this sub.

Human skulls are formed as multiple different bones, however, during childhood each of those bones become fused together along suture lines. This ultimately results in one solid structure. The exception to this rule is the mandible (jawbone). The jawbone is not actually fused with the rest of the skull, as this would directly inhibit your ability to chew/speak/etc. Instead, the condyle (the bump you can feel forward of your earlobe when you open and close your mouth) articulates with the temporal bone. This means that the two are in contact, but are not actually attached to each other. The only thing which actually holds the jaw in place is soft tissue, of which there are many structures anatomically however, suffice it to say that all of these soft tissues eventually decompose after a person has died. As a result, the mandible of a skeleton is now only held in place very loosely by pressure between the condyle and the temporal bone and can very easily pop off. As a result, most of the skulls that I have personally interacted with have the mandible separate from the cranium as it tends to readily fall off, even from something as simple as resting the skull on a table. Because of this, it would make sense that the mandible is liable to be lost/misplaced or simply discarded due to the hassle of constantly keeping it in its appropriate anatomic position once the supporting structures have decomposed.

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I understand that this is more of a medical than a historical answer, so if this answer requires additional information to be considered acceptable, please let me know and I will try to amend it, or simply remove it as the mods see fit.