Why is my inbox count in gmail and apple mail different?

Yesterday, I asked my wife to go to gmail.com and clean up my inbox because I had over 500 messages in there. She logged into gmail.com using my email and password and she cleaned it up to only have 12 messages.

I wasn't aware that she had finished because all day, my apple mail that is linked to my gmail showed the same 500 messages. When I came into work this morning, I noticed that it now says 249 messages so it did, in fact, delete (or archive) some of them. I'm wondering if the only ones that updated are the ones that she deleted but not the ones she archived.

So my question is what am I doing wrong with my settings. Is there a setting messed up where archiving messages in gmail.com doesn't archive them in apple mail or visa versa or is the whole thing just not syncing correctly?

Thanks,

Caleb