MC1.15.2
Using latest stable dev build (#4573)

When creating a custom crafting recipe, the minecraft:player_head is not recognized as an input item. All legacy variations (head:3, head_item:3, skull:3, skull_item:3) are translated into unrecognized items (stone) as crafting or furnace recipes. Using player_head as an output item works just fine (whether it has a skin specified or not), but as an input item it shows as unrecognized stone. Flattened zombie_head, creeper_head and wither_skeleton_skull input ingredients are unrecognized, as is any player_head with a defined skin, however work as intended as outputted results.

For instance this recipe, which should accept any variation of a player head regardless of skin as an input item, instance only accepts skeleton_skull items as an input, but outputs the generic player_head like it is supposed to...
cookedhead: type: Furnace ingredients: 'minecraft:player_head ': 1 cook-time: 500 experience: 0.5 results: 'minecraft:player_head ': 1

Using legacy item IDs such as the following, instead requires 3 unrecognized Stone as an input ingredient instead of a single player head item...

cookedskull: type: Furnace ingredients: 'minecraft:skull:3 ': 1 cook-time: 500 experience: 0.5 results: 'minecraft:player_head ': 1

PS- The server was restarted (shutdown, wait, Start) for all testing and recipes are not properly reloaded.

This was probably fixed by Spigot in 1.16 with their recipe fixes.

If that doesn't resolve it, it's still a spigot issue either way.