Between at least the 18th into the 19th century, anatomical specimens (cadavers, skeletons, bones, organs, etc.) were regularly produced by grave robbing or outright murder (see Rosner's book on the Burke and Hare case.) Though this practice began to subside with "anatomy acts" legislated in the 19th century in the UK and USA, which attempted to curb grave robbing, the source of human bodies for scientific learning and research was replaced by the use of unclaimed bodies or the bodies of the working poor and otherwise indigent (see this book by Richardson.) In other words, it would be assumed that the bodies provided by Holmes (or anyone else in this era) were individuals that were essentially 'forgettable' and expendable to the cause of medical science. Perhaps even worse, there may have been some suspicions that the bodies were those of murder victims, but a short supply of cadavers or skeletons could lead university officials to turn a blind eye to the source of specimens. Universities might have also intentionally kept no records on the source of skeletons to protect themselves from claims of "body-snatching" or accepting body parts from murdered people (and likely didn't ask the source, either.)

Further, universities and/or medical schools at this time did not have a set of universal research ethics or consent procedures for the use of human specimens. It wasn't until after WWII that contemporary clinical ethics truly started to take hold, and people began to voluntarily donate their bodies to science. In other words, faculty and staff in 19th century medical schools did not have the same idea about body donation and respecting the intention of the donor as we do today; they were much more opportunistic when acquiring specimens, and didn't necessarily pay much attention to where the body came from.

Source: I've spent many months doing ethnographic research in a human gross anatomy laboratory, and my MA thesis was on early modern dissection in Europe-- I can provide further reading if interested.