Using productivity modules in the Liquid Tiberium Fuel Cell recipe causes a surplus of empty fuel cells.
For example with 30% productivity on filling the fuel cells:
1 empty fuel cell -> 1.3 full fuel cells -> 1.3 used fuel cells -> 1.287 (1.3 * 0.99) empty fuel cells

I think the yield rate on the refurbishing recipe needs to be reduced.

Edit: corrected productivity to 30% since it's made in a chemical plant

Sounds more like making the fuel cells shouldn't be allowed to have productivity.

Why? It's not like using productivity makes Tiberium nuclear power unbalanced, 30% productivity only raises the energy per liquid Tiberium from 12.5 MJ to 16.25 MJ - which is still below the 25 MJ that the Tiberium Power Plant gives. Removing productivity would put it in line with the regular nuclear fuel, though I am not sure why this mod doesn't allow productivity there.

Personally, I feel like the refurbishing step is redundant because you only have to produce 1 new cell for every 100 cells consumed (on average), but perhaps that's a different issue.

I feel like the refurbishing step is redundant because you only have to produce 1 new cell for every 100 cells consumed (on average),

Refurbishing does more than make you have to create new cells.

What's the other purpose of refurbishing? The minuscule sludge output?

The logistic problem of having to deal with dirty cells.