To reproduce, unlock any recipe: /recipe give @p minecraft:tnt. Now remove that recipe: /recipe take @p minecraft:tnt.

The recipe will still be visible in the crafting interface in a crafting table, and can still be crafted even with /gamerule doLimitedCrafting true. Exiting and re-entering the game properly removes the TNT recipe and disables its crafting if that gamerule is true.