Will PhD rejection return to haunt later?
What was written down on an application years ago will generally not come back to haunt a faculty candidate later. However, actions that might have been taken on a faculty visit—or in later interactions with faculty members at a department—could have repercussions.

If the reputation that someone builds is being a person who "doesn't play well with others," that will be a tag that follows that individual for the rest of the career. It can make life a lot more difficult, because that person will have to work a lot harder and be a lot more successful than someone who is able to interact with current and potential future departmental colleagues in a civil and cordial manner.

But what's written in an application? Unless it's fraudulent, it shouldn't have a bearing on future ability to get hired somewhere.