In my experience, massacre missions issued by different factions, targeting the same factions, will stack.
Example 1:
You accept pirate massacre missions from Factions A, B, and C.
All missions target Faction V, in system 1.
Kill 1 Faction V pirate in system 1, it counts toward all missions from all factions.
Example 2:
Accept 2 massacre missions from Faction A, and 1 each from Factions B and C. All target Faction V in system 1.
Kill 1 pirate of Faction V, it will count toward 1 of the Faction A missions, and both missions from Factions B and C.
Example 3:
Accept 3 massacre missions from Faction A, targeting Faction V in system 1.
Each kill counts toward 1 of the missions only, in the order the were accepted (oldest first, I think.)
Happy hunting, Cmdr.
