Yeah I use a web app regularly for work where they have implemented their own "back" button in the app. The app maintains its own state and history so the browser back button is totally broken.

The problem here is that they've implemented an application navigation feature with the same name as a browser navigation feature. As a user, you know you need to click "Back" and your brain has that wired to click the broswer back button.

Very annoying.

Having "Refresh" break things is (to me) a little more tolerable. I have the mental association of "refresh" as "start over" and so I'm less annoyed when that takes me back to some kind of front page in the app.