When fueling the locomotive with lava it consumes the bucket as well.
I suggest making an output slot specifically for empty buckets or some sort of internal inventory where either extra fuel can be loaded or spent fuel/fuel items (depending on the other mods used) can be moved too.
Being able to automatically remove said items with a hopper underneath would be nice too.

This is partially fixed in the 1.20.1.1 release (buckets no longer disappear). However, it is not currently possible to remove the buckets from the inventory. There are some plans to rework how containers (items/fluids/energy) are exposed to hoppers and item transfer blocks, but that is not currently complete or finalized yet.

Going to keep this open to track the "remove from bucket" sitch