You have probably run into what seems to be alternate spellings of common words.
Here are some common examples:
If you are a British student submitting a paper to your British university, chances are you need to keep your spelling consistent with British standards. The opposite should be true if you are in the United States.
Proofreading Tool keeps track of overall spelling patterns used in your writing, and will let you know if there are any inconsistencies with regards to American versus British spelling. The grammar checking software will flag all potentially conflicting cases and then give you the option to standardize them all according to one standard or the other.
For example, if you are American, then you will generally use American spelling without a second thought. However, Proofreading Tool will catch that rare occasion when you type out "recognise" instead of "recognize" and then highlight all potentially conflicting cases. At that point, you can select the option for whichever standard you need (American in this case), then click the button to proceed and correct all the flagged cases in your document.