Fade In is, like other professional screenwriting software, designed to produce output with industry standard markup for revisions, indicating changes between drafts through page colors, markers for changed lines/sections, etc.
Normally you will turn on revisions by setting the current revision level under Production > Revisions. The default revision level is white pages, i.e., no revisions. Setting the revision level to a higher level/color will result in revisions being marked with the selected mark in the margin (by default an asterisk, "*").
You can also use Document > Compare to Previous to create a separate document showing differences between two documents by highlighting additions and deletions.