What do I do if my advisor made a mistake? I am a first year masters student and I am just beginning my research project. I had to send a protocol out to my committee and they all have to approve it before I begin the project. The protocol is basically a document that states, step by step, how I will be completing the project. It will be published once my committee reviews it.

I have went through several drafts of my protocol and my advisor has reviewed and edited each draft. So the one I sent out to my committee was the good copy. I told all my committee members that I would like it back within 2 weeks. My advisor is out of the country for 3 weeks, but she just sent me her comments on my protocol last night. However, she ended up reviewing one of my old drafts again. I double-checked the email I sent her, and I definitely sent her the good copy I wanted reviewed. 

I'm not really sure where to go from here. Should I explain her mistake to her? Or just send her the good copy and say I revised it?
Just tell her, mistakes happen.

Dear Prof. OutOfCountry,
thank you very much for your comments and review, but it seems that you reviewed an older revision of the document. Find the latest revision attached.
As you can see, most of your points are already addressed in this revision, as well as the following major changes:
[...]
Regards, aspire94