Similar to the actions taken on Bug 11360, when scanning in returns, it can be easy to miss a transfer message due to the fact that the barcode and submit are still active and the barcode field is focused on. When a librarian is quickly scanning in returns, it is easy to scan another item and pass over the form to accept the transfer, which is equivalent to clicking the "ignore" button.
I believe this has been resolved since filing by our use of modals in the circulation module.