I was able to review some of the related cases, and it mentioned that it is possible that you have marked elimination to some inventory accounts such as Inventory in Transit. Can you check?
- Navigate to Lists > Accounting > Accounts
- Find account Inventory in Transit and open
- Check if the Eliminate Intercompany Transactions checkbox = True
Based on the related case and if the Inventory Transit is set to True on your account, it is not necessary to mark it as Elimination since this account is supposed to be used by non-intercompany transactions (such as normal transfer order) and intercompany transactions. As per SuiteAnswers 48689, when you enable Multi-Location inventory, this feature creates the system-generated Transfer Orders and Inventory In Transit accounts.
As for the determination of elimination transactions, it is normally depending on the transaction type. In Advanced Intercompany and Intercompany Journal Entry, you can manually click the Eliminate checkbox unlike in other transactions – However, for Intercompany Accounts Payables/Receivables you need an Intercompany entity. For intercompany Sales Orders and Purchase Order you need to be able to assign it to an Intercompany Customer or Vendor respectively in order for it to be considered as an Intercompany Transaction. In Intercompany Transfer Orders, you need to create it from the form itself since you need to identify the subsidiary you are transferring it to.
Now, your issue may not be limited to Inventory in Transit. Please check if your other accounts in the item record please check your other non-intercompany accounts such as Gain/Loss Account etc.