If you place a Gas Refinery and then pick it back up, it is picked up as an Advanced Gas Refinery which is larger, uses more power and has a lower crafting speed.

Additionally, some mods add multiple ways to smelt a given output, which can result in the same inserter mis-match problem. e.g. Angel's ores adds smelting crushed saphirite to make iron plates, but you can still use iron ore to make iron plates. The crushed saphirite recipe takes 2 input to make 2 ...