Hi John,
Which version of the Web GUI are you using? Is the auto-refresh placed on a Main subject and does it have details? When Auto-refreshing the main subject, details of the selected row are refreshed too as due to changed values, it may cause details to be not visible anymore or have different data after the refresh action.
I believe the Auto-refresh should stop when you are in Edit mode but I may be wrong. Alternatively you could look into Change Detection logic. This fine piece of functionality can tell the GUI to continue Auto-refreshing at its given interval or not based on SQL code. More on it here: https://docs.thinkwisesoftware.com/docs/sf/business_logic#change-detection