Canon BJC 3000 Reference Manual page 285

Check 1
Did you place an image within the proper scanning area?
Check that the image you wish to scan is placed 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 the image you
scan, parts of the image will be missing.
If you place the image outside the scanning area mistakenly, parts of the
image may not be aligned properly. Always check that the image is set
within the proper scanning area.
Parts of an image are missing or not aligned properly
Troubleshooting - Scanning result is unsatisfactory 285