Spigot makes some things work kind of weird, for example, the enderman farm is really slow compared to how fast could it be in Vanilla/Craftbukkit minecraft, I don't know if there's a fix for this, but it's kind of annoying, it also makes iron farms to work way slower or to not even work :/, lastly, I would like to add that this is not a complaint, it's just a suggestion :>
When I last played the Enderman farm appeared to be working stupid fast - it's possibly it got blocked up, or something is preventing spawns (if someone's on the main island endermen will spawn there). Iron farms are generally super slow, from my experience. I doubt any of this is Spigot's fault, as Spigot actually adds several optimizations to vanilla, resulting in faster operation overall.