[remram]

Yes, this month emails in my organization have been marked as spam. Those are emails from an @nyu.edu account to another @nyu.edu account, sent from the Gmail webmail, and nyu.edu is a (big) Google Apps domain.

I don't understand how this happens.

[ghusbands]

That happened for us (basically the same situation) many times over the whole time we used Google Apps, and I've seen other reports of the same over the last five years. It probably happened more than we noticed, because we only noticed when people happened to follow it up via some other mechanism. It also happens to non-commercial users - emails sent as a reply from gmail webmail to gmail in an existing conversation sometimes get spam-binned without obvious reason.