It sounds like you already have a very good understanding of what type of iPhone activity in a non-WiFi environment should create data charges, and that you have selected the right Settings to keep from using "Cellular Data".
If your Cellular Service provider is one of those companies that has an iPhone App that you can use to check on your charges / usage when ever you want, you should download and use that App.
My daughters are on my Cellular Family Plan (even though they are fully grown and have families of their own) and they have discovered it only one or two TV Shows or Movies to use up our Monthly Data Allowances provided by our plan ...so they typically only watch those items in a WiFi Network environment. A couple of times though they were amazed at how quickly they got the warning "Free" Text from our Service Provider saying they had used over 50% of their monthly allowance.
If you take your iPhone out of the WiFi network and have Settings>Cellular>Cellular Data "On", you don't have to actually view your email to have Data Usage ...that is if you have "Push" email checking. Also, seen threads in this Community Forum where iPhone Users were getting Data charges at night as their iPhones were charging. You could search and find some of those threads and their Solutions, in the event that is what you are experiencing.
It is possible, that your Service Provider may be able to help you discover the timing of the highest volume of data charges in your case. Then you could probably learn how to mitigate the issue and ensure you don't get surprised by future Data Use and Charges.
Good Luck toward learning the cause. Again, it sounds like you are very aware of effective Settings and of the features that could cause charges, but it will be well worth your time to see if your Service Provider has information that will give you an assist.