• Create a stirling engine
• Attach a pipe to it
• Attach an emerald gate to the pipe

If you put a single piece of coal into the stirling engine "inventory full" is active on the emerald gate. Also "space in inventory" is inactive.

I would expect this to happen when there are 64 pieces of coal in the engine, not 1.

Buildcraft 6.2.0
Forge 10.13.2.1232
Railcraft 9.4.0.0

I think that is indeed how Inventory Full and Space In Inventory works. If you try it with a chest, the "Space In Inventory" trigger will continue to be active up until the very last in the chest is occupied. When the last slot is occupied, the inventory is considered as "full". Same case here with the Stirling Engine, since the engine has only one slot inventory.
I recommend to use the "Contains<% of item" trigger instead.

RagaRBM is correct. Another option is to use a gold gate so that you can add a parameter to the Trigger. That way "Space in inventory" will be active all the way up to 64.