killed a shifter with the song apocalyptic overture and afterwords I could not make a trophy of the corpse but another villager could. The specific situation was we both hit a group of 3 together and I hit the killing blow on the shifter but the groupmate was tanking.

It's impossible to say without knowing more of the circumstances, but it's probably by design.

For example, if you kill the same guy twice in reasonably quick succession, the second corpse is unworthy of a trophy.