It seems you have extra Memory MB on your two machines. The free allowances include:
You can fix that by running fly scale memory 256 -a APP_NAME
As for the other line its a preview charge and it can be better explained here: We are going to start collecting charges for Stopped Machines RootFS starting April 25th
There we talk about how to prevent charges. One of those ways: just let your machines run 24/7 (aka disable auto_stop).