On my multiplayer server a few friends and I have created an EXP farm out of a Sea Temple, removed all blocks and replaced with water with bubbles from soul sand. It all started working perfectly fine, but after a day or two it suddenly stopped spawning all guardians unless we relog onto the server and we get around 15 spawns until it runs dry again.
We have not messed with it after we finished it but tried fixing things without any fixes, if I could be told we're just silly or if this is an actual issue, that would be great.
Here's some pictures for all to see, From where we stand for the kill pit and what it looks like.
Have you checked the 128 block radius of each player to see if there arent any places where other mobs can spawn? Have you tried a /kill @e to kill them?