This is not normally a problem (eg lava bucket is unstackable->only one at a time, coalblock is expected to be consumed) but using a stackable fuel source that returns an item (eg empty glass bottle) causes the formspec to bug out a bit and the "returned" item is not returned anywhere until the slot is empty where only a single "returned" item is actually returned.
Glitching: "Split stacks" toggle and (empty) fuel-inventory blinks.

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Link to upstream issue: minetest-mods#543 (comment)