I noticed this too. And a raw gem is worth more than a polished gem... Looks like to the shops, labor has negative value...
In the case of coal, you might somehow justify it in that it could also be used for higher-tier recipes, and that flexibility is lost. But even so, there's no justification for this sort of negative value on labor.
The logical thing (at design level) would be to assign each crafting Tier some value for 1 AP of labor; crafted materials would have the base value of the raw materials + labor required to make them.