The title pretty much says is all. one of often used used folders in my fish terminal suddenly became highlighted in yellow. Most of it's sub folders are highlighted in yellow too. Not sure what happened.
it's on mac Yosemite
Fish shell highlighted those directories yellow because that directory's permissions is set so that everyone can read, write, and execute. Essentially fish shell is warning you that the directory has the least restrictive permissions in case you weren't aware.
For example, in this screenshot:

chmod 777 oranges/), then you can see fish shell adds the yellow highlight.chmod 775 /oranges), then the directory "orange" is no longer highlighted.Here's a good explanation of file permissions and the command chmod for more detail.
When you say "highlighted" do you mean when running ls? Probably you have $LSCOLORS set to something ugly.
Here's how you can set it to something nice, in fish:
set -Ux LSCOLORS gxfxbEaEBxxEhEhBaDaCaD
which makes it look like so:

(Just run that command once, don't put it in a startup file or anything)
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