Don't worry about word-level problems in drafting
As the word count grows, you say, so I am going to assume this is your first draft.
Don't worry about details on this level when writing the first draft. YES! Don't be F-ing ctrl-F-ing when drafting! ;)
Actually, don't worry about anything else than writing the draft. The first draft is a pilot for your final story, a beta, or even a gamma. Maybe it's one enormous experiment in brainstorming? Whatever it is, it's not the final draft. The first draft is never the final draft.
At this stage, maybe all you'll get is a beginning feel for your characters and their voices. Maybe you'll actually have a solid story when it comes to structure and plot, but not so much more.
Don't be surprised if you need to send a bunch of your characters to voice training camp once editing starts... not to mention teaching them to stop nodding all over the place, or mumbling or smiling or laughing once in every chapter... Or obsessing about each other's eyes... Ack!
Finish writing your first draft, then start the editing work.
Worry about favorite phrases late in the editing process
Once you start editing, there will be far larger things to deal with long before you get to any word usage problems.
Below is an approximate priority list (based on James Scott Bell's "Revision and Self-Editing for Publication" with adjustments from a handful of other sources). The most important actions come first and the least important last.
- The overall impression of the story; can it be molded into something that works?
- Characters, their arcs, likability, etc. Is your protagonist worth following for a whole book?
- The structure, acts, subplots, the beginning, middle, and end
- Scenes, paragraphs, and sentences; perspective, dialog, showing and telling, character voices and style, settings, descriptions
- Details on the word-to-word level, e.g. passive-active, power words, adverb and adjective removals... and also, finally, looking into repeated words and favorite expressions
As you work your way from 1 to 5 in this list things will get cut, scenes, characters even whole subplots.
It's easier to cut things if you haven't spent hours polishing them.
Also going down the list, words will be changed and a lot of repetitions may be removed.
For instance, fixing character voices and problems with showing and telling will introduce a larger variety in word usage and remove a lot of words related to telling.
If you use deep perspective, you have another source for word removals:
- He thought the house was too warm → The house was too warm
- She thought she saw the shadow moving → Was the shadow moving?
The same goes for dealing with adverbs and adjectives, consider for instance:
- A small house → a cottage
- A large house → a mansion
- An extremely tall house → a skyscraper
Three fewer usages of "house", just there... You get the gist...
Brainstorm, and make lists
You'll still have repetitions, though. But likely far fewer than when editing began.
You can solve this by brainstorming lists.
Create a list of ten things to use instead of that expression that keeps coming up. You may get stuck at three, push through to ten anyway, be crazy, obnoxious, silly... then let it simmer for a while before you reject it, maybe there's a golden nugget in there anyway?
Having problems describing a place? Can you visit it, or someplace similar? Maybe you can't visit your Elf-character's magical forest but you may be able to visit a real forest...
Even though online images and videos won't give you anything but visual and sound, the Internet can also be a source for variety in descriptions.
Finally, as mentioned in other answers, don't forget that a few characters may be nagging repeaters... You might need outside help from beta readers or editors to determine if it works or not.