So I'm not sure about the full conditions for this but I have a repro case that works consistently.
- Equip helix and skewer mods and gear for at least +100% mod power gen, so the reaction chain refund gives a full charge back for the other mod.
- Fire both charges of helix, then fire off both charges of skewer. The skewer casts will properly refund helix casts.
- Fire both charges of helix again. The first cast fails to refund, the second cast works fine.
This works swapping the order of mod casts, so it doesn't seem to be a bug specific to one of these two mods.