This issue is most prevalent with mystic agriculture but here's an example using wood essence to make various different types of wood

trying to make cherry wood, this is the recipe in JEI:

This is what the crafting terminal tries to provide (mangrove wood):

This is the actual recipe for Mangrove wood:

Because of this odd behavior it causes numerous recipe conflicts that wouldnt otherwise exist because these recipes are all shaped recipes.

The actual recipe definition from MA's source is

{
  "type": "crafting_shaped",
  "neoforge:conditions": [
    {
      "type": "mysticalagriculture:crop_enabled",
      "crop": "mysticalagriculture:wood"
    }
  ],
  "pattern": [
    "  E",
    " E ",
    "E  "
  ],
  "key": {
    "E": {
      "item": "mysticalagriculture:wood_essence"
    }
  },
  "result": {
    "id": "minecraft:cherry_log",
    "count": 16
  }
}

Let me know if I can provide any additional info, ty!

This is an AE2 bug, not a JEI integration one as it seems to be filling correctly