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There could be several reasons why your findOneAndUpdate query is not removing items based on ID in MongoDB:

1. Incorrect query parameter: Double-check that you are passing the correct object ID as the query parameter for the findOneAndUpdate method.

2. Incorrect update parameter: Ensure that you are using the correct $pull operator with the correct syntax to remove the item from the array.

3. Incorrect schema definition: The issue could also be with the schema definition. Make sure that the schema is defined correctly and that the array is defined as a valid array.

4. Lack of permissions: Ensure that the user executing the query has the necessary permissions to execute the findOneAndUpdate method.

5. One-to-many relationship: If the ID you are using to remove an item belongs to a document with a one-to-many relationship, you may need to reference the parent document and then execute the findOneAndUpdate query on the child document.

6. Versioning issue: If you are using versioning in your schema definition, ensure that you are updating the correct version of the document.

7. Error handling issue: Check if there are any errors being thrown during execution of the findOneAndUpdate method and handle them appropriately.