Equations cause wrong error messages in spelling check in Word, how to avoid?

Word lets you insert what it calls a "no-width non-break" character via Insert->Symbol->More Symbols->Special Character. This is Unicode U+200C, known in Unicode as ZERO-WIDTH NON-JOINER.

If you insert one of those immediately before the "y" equation it appears to prevent this particular error from being flagged.

Not ideal, and when it comes before the equation, the character looks as if it's inside the equation "box" (although it isn't).

The OP has commented that it needs to be used carefully, e.g. because used after the "y" it may act as an optional line break, pushing the "." onto the next line.

If you are comfortable with it, you can turn off the grammar check for punctuation. This will prevent this "error message" from appearing, but will also discard other suggestions about punctuation (such as improper use of semicolons, etc.)

In Word 2007/2010, this can be done in the Proofing Options:

I am assuming the option is the same or very similar in Word 2013, which you are using. I am not aware of an option to disable this just for cases involving equations, and I don't think that it exists.