We all have crutch words--those words that seem to crop up in a manuscript, edging out other, more useful or appropriate words. Some of them seem to be the equivalent of the spoken "um" merely vamping until thoughts coagulate. I have a list, but even after I cull my known offenders, others seem to be sucked into the manuscript--after all, nature abhors a vacuum.
I've started trying to search and destroy these words as I go, checking every few chapters. Easier to cull 50 appearances of "just" now, than 500 of them later.
But sometimes, there's a word that will be repeated simply because it IS the best word, and to start substituting makes things even more awkward. A door is a door. How often do people go through portals? If it starts to sound like your digging through a Thesaurus to avoid repeating a "limited function" word, you might be better off repeating it.
