How AWS calculate hours usage?
There's nothing complex here. One hour of EC2 t2.micro usage counts as one hour of free tier usage. EC2 billing is per minute, but it's possible that if you start and stop an instance free tier counts it as an hour. Generally EC2 instances are long lived, rarely stopped and started, so it shouldn't be an issue.
If you run two t2.micro you can run them both for half a month. You probably have multiple EC2 instances running, maybe in another region.
Tracking Down Instances
Check AWS cost explorer in the billing area. AWS Console -> top right menu -> my billing dashboard -> Cost Explorer -> Launch Cost Explorer -> Cost Explorer (left menu). It's weirdly difficult to get into.
Once in Cost Explorer click "service" on the right - click the word service not to the right. Tick "EC2-Instances" then "apply filters". From there you can click "usage type" at the top of the graph. Then look below the graph at the list.
If you can't work it out please edit your post to include screenshots of cost explorer.