in CS01 you can probably click enter to accept the message and to continue, in a background program you can't do the same.
Did you already try to change the message settings to warning or hide, this setting is in IMG > Production > Basic Data > BOM > General data > change message...
Have you somewhere in your CSAI_BOM_MAINTAIN a KZKUP field? If the quantity is negative then it means you get it out of production which is usually a by-product and KZKUP should have an entry.
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