Per se is a Latin expression which means "in and of itself". The se is pronounced to rhyme with "say", but it isn't spelt that way. Someone urgently needs to tell the internet.
It's understandable how this error comes about — if you've only ever heard the expression, it's unlikely you would guess the correct spelling. And that's why we see the wrong version pop up in news reports:
"I don't think it's the temperature, per say," he said.
No, he didn't say that.
One tactic to consider is to always place the expression in italics, indicating its origin in a foreign language. While per se is arguably so widely used that this isn't a strict requirement, it will draw the reader's attention to the fact that it's an unusual phrase.
Another solution is not to use it, replacing it with "in and of itself" or a similar phrase, or rewriting your sentence entirely. That will potentially make it easier to read. But if you do decide to use it, spell it correctly. Accuracy matters.
Lifehacker's Mind Your Language column offers bossy advice on improving your writing.