The most common reason for this is incorrect subject mappings, whether deliberate or accidental. 

For example, you may be importing 9-1 grades for English Language, but you have accidentally chosen the A*G version in the subject mapping. The easiest way to check is to click on a grade in an affected column and look at the available options to change to. 

If you need to amend your mappings, go back a step and re-map affected subjects.