In our ERPNext v16.21.1 setup, a Job Card creates a Transfer Material Stock Entry using an Alternate Item to move raw materials to the WIP warehouse. After the Job Card is submitted, clicking Make Stock Entry for the semi-finished transfer still uses the original BOM item in the consumed materials list instead of the alternate one.
This results in an insufficient stock error because the BOM item is not available in WIP.
Please check whether this is expected behavior or a bug.
