Given that you're working with the file in vim, you can fix this within vi/vim too. You can type these character with ctrl-v, then ctrl-. For this, it's crtl-v, followed by ctrl-f.
So, you can use a simple find/replace:
That would work on all lines (the %), and replace (the s), the first instance of ^F, with nothing, effectively removing it.
If you want to see hidden characters in files, instead of cat, try using od -c:
od -c <file name>
eg, but putting a ^F and two line-endings in a file:
alex@Smiley:/tmp|⇒ cat test
alex@Smiley:/tmp|⇒ od -c test
0000000 006 \n \n
This prints out all characters escaped, including tabs, line endings, etc.
If you want to use sed, you can use the same ctrl-V, crtl- trick right on the command-line too. That way you don't need to remember the translation.