Will PhD rejection return to haunt later? Suppose a student applies for PhD at a university and his application is replete with problems: average academic record, poor SOP, so-so recommendations, etc and he is rejected outright. He gets an admit at another university, does very good work and completes his doctorate successfully. Now he deems himself to be a fit for a faculty position at the university which rejected his PhD candidature.

Will his past mistakes come back to haunt him? Will the university dig up his PhD application and count this against his faculty application? Or will he be judged by his work during the course of the doctorate alone?
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.