Unfortunately most likely what you saw is what they will but I'm pretty sure HR departments are used to wonky formats happening.
Assuming you're using Word some ways I've found to circumvent the issue are to:
(I'm going to assume you know how to copy/paste and rename files...if not, let me know).
1) Make a copy of your resume and rename it changing ONLY the letters to the RIGHT of the <dot> to doc
You'll get a pop up saying that changing the format may make it unreadable, click 'Yes', you're sure you want to do that.
Now double click and it should open in Word. Clean up the formatting then click 'Save' NOT Save as <select the format>
You now have a cleanly formatted version of your resume in .doc format.
2) No need to make a copy of your resume for this one, you'll be uploading it but not changing it: Use a free pdf converter to make a copy of your resume in pdf format. I've used both Online*PDF*Converter
and Word to PDF Converter – 100% Free
recently without any problems.
Something else you may want to take a few minutes and do is convert your resume to a .txt file, as archaic as it is I've encountered some employers who still want that format.
Open Notepad on your computer, now copy and paste your resume from Word into Notepad.
From there you'll be able to clean up any formatting and weird symbols (any bullets, etc used in word don't translate into .txt)
When you're done select 'save' and name it.
All my resumes files are named using my first initial and last name, the only thing that is different is the extension: .doc, .docx, .pdf, .txt.
Another 'cheat' I use is to create a master list of all the information that goes in an application in .txt format so I can copy & paste it into the online app. It's especially helpful for those little boxes where they want you to describe the job duties (that are listed so well on your resume). Those boxes usually have a character limit so it helps to have that info all typed out succinctly to just C&P in...no reason to set yourself up to run out of room or make a typo where you can't spell check.