When replicating a fluid, and the cells are in the correct slot, if there is no fluid in the tank, but cells in the slot, when the process is complete, and the fluid is replicated, the fluid is added to the tank, then removed, and a cell is placed in the lower slot. The issue is that this cell doesnt contain fluid, instead it contains "minecraft:fluid_empty".
As long as there is already a fluid cell in the bottom slot, or more than 1000mb of fluid in the Fluid Replicators tank, lava cells will be produced as usual. If one of these fluid_empty cells is in the bottom slot, but not removed, the machines internal fluid storage will continue to fill up, and then will produce fluid cells as per usual once this bottom cell is removed, and there is more than 1000mb of fluid in the tank.