Seems to me that the issue is in the integrations. Its sounds as...

Seems to me that the issue is in the integrations. Its sounds as though they have 2 systems running side by side and they are struggling to consolidate the two. Why else will 2 orders go out unchecked? There must be some legacy systems running that are confusing the situation
It doesnt sound like a coding issue with the platform, if it was a coding issue it'll likely be across the B2B network as well. If it was a coding issue it should have been solved a long time ago.