Please check the following points.
Has the document been properly folded in half?
When scanning thick documents, the two images have a tendency to skew outwards from the top.
Place the document snugly against the Carrier Sheet edge.
Feed Carrier Sheets into your ScanSnap with the closed end facing the scanner.
Depending on the way to set the document in the Carrier Sheet or the effect from the friction, some parts of the image data to be lost. In this case, this issue will be improved if the document is set a little inside of the Carrier Sheet frame.