The GAE Flexible environment instance resources are charged on a per-second basis with a one-minute minimum usage cost. Which means, if you have a resource(Ex:1GB RAM) attached to a GAE flexible environment, its usage is calculated as follows:-
Using 1 GB of RAM in your GAE Flexi Environment cost = $0.0071/hour (as per the doc.)
For a day $0.0071*24 = $0.1704
For a month $0.1704*30 = $5.112
You can also use the ‘Pricing Calculator’, to get an estimate of your usage as well.
After calculating your usage cost and still, you have any discrepancy, I would strongly suggest you to contact the billing team for further clarification.