Enter digit instead of checkmark in box with Preview
From the Annotate toolbar (shown by clicking the pen icon), choose the Text tool. This inserts a text box into the document, which you can type characters in and reposition where you would like the characters to appear in the document.

              

The default tool, text selection (highlighted blue on the left of the above screenshot) will automatically enter a check mark in a box it determines to be a checkbox. You need to manually add text boxes where you wish text to appear if the assumption by Preview is incorrect.