This is a very simple yet annoying bug. When you use EnderCrystal#setBeamTarget with a location with non-whole numbers, the end crystal instead uses a whole number for the location.

Attached is a very simple reproduction plugin that spawns 2 end crystals, one pointing at 0, 5, 3.25 and one pointing at 0, 5, 3. These both actually point to the center of block 0, 5, 3 in-game.

also its end crystal not ender crystal