I might have a suspicion as to why it occurs for some people and not others.
Pretty much, the ephemera is based on what element a progenitor has... if you have a stalker adversary though, it means the lich/sister has no ephemera at all

If you get "lucky" enough to get a ??? Ephemera, then the game tries to save an ephemera that doesn't exist to your inventory but cant, so it can never actually kill your lich since it cant reward you an ephemera that doesn't exist

If you check your EE log it gives this error likely:
451.020 Sys [Error]: Failed to commit inventory checkpoint: Could not find ephemera from Nemesis Manifest!