Canon S400 Reference Manual page 227

Check 1
Did you position the original within the proper scanning area?
Make sure the original is positioned in the proper scanning area.
Check 2
Did you specify the scanning area correctly?
If the Paper Size setting is smaller than the paper size of original, parts of
the image will be missing.
If you position the original outside the scanning area mistakenly, parts of
the image may not be aligned properly. Always make sure the original is
positioned correctly.
Parts of an image are missing or not aligned properly
Troubleshooting - Scanning result is unsatisfactory 227