That does not seem like a bug, but rather a reaction to the mechanics changes between 0.40.24 to 0.43.05.
In 0.40.24 all non dwarven, non pet corpses were treated as refuse and stored in the refuse stockpiles (scaring traders and citizens).
In 0.42.01 onward all sapient corpses now are stored in the corpse stockpile, with the exception of corpses of formerly sapients that have been reanimated: these corpses are considered refuse and do no longer induce horror beyond that of ordinary animal corpses.
Thus, you probably have to reengineer your burial grounds to handle the additional volume of corpses (and parts thereof), possibly including destruction methods. Unfortunately, the change of the mechanics were not followed by means to separate corpses: the corpse stockpile has no sub categories.