Lookup Filter behaviour in LEX.

As per the Considerations for Lookup Filters documentation:
In Lightning Experience, a lookup filter doesn’t work if a field referenced in the filtered lookup criteria isn't added to the page layout. When a user opens the lookup dialog box, the value being searched is automatically deleted. To avoid this issue, add the missing field that is being used in the lookup field filter criteria to the page layout.

To resolve this issue, ensure that the fields—especially standard fields—specified in the lookup filter criteria are added appropriately:

• For Lightning Record Pages: Add the required fields to the Page Layout associated with the Lightning Record Page. If the Record Detail component has been upgraded to Dynamic Forms, manually add these fields using the Lightning Record Page Editor.
• For List View Inline Editing: Ensure the required fields are included in the 'Select Fields to Display' settings.