Important is the time of PO creation, not the goods issue.
SAP is comparing fields ekpo-bwtty with mt06e-bwtty, for example in program MM06EFPO_POT_LOESCHEN
and mt06e-bwtty is either the BWTTY field from MARC or MBEW, can't say it without system access today.
And if your EKPO BWTTY field has different content than the same field from MARC or MBEW then then either the material master has been changed after PO creation, or someone has changed the purchase order item (in the PO is the field not at all open for maintenance, it is copied from material master at PO creation)