InternalRuleFired events will say which rule made it fire with the InferrenceRule field. I would suggest you run a ndepth query to look for that event in the timeframe that you see the email firing or look at your filter for Internal events and look at the InternalRuleFired event
Also if the InternalRuleFired event is in your filter you can explore that event and see what it fired and what made it fire.
I would suggest taking the time to go through your E-Mail templates and making them less generic. In other words, if a rule triggers and E-Mail, that E-Mail should contain enough information from the event to tell you what rule it came from.
My issue is using the "default" email template. I am working on customizing the email templates as it goes now. thank you.
I always include the alert name variable at the bottom of all alert emails. It doesn't mean anything to the recipient but it sure helped me when people start asking why they are receiving particular alerts.