One SQL Server RDS instance plus one Ubuntu instance cost money on my initial free trial year
Yes technically both are considered separate instances.  However you get 750 hours free for each as they are billed as separate services with the caveat that instance sizes have to be a t2 micro.  Since RDS is a managed service you won’t see the running instance in your ec2 console even though it’s an instance running in your account. 

Some things to look at on your bill as they might be the cause of the charges:


Are you using more than 30gb for EBS volumes attached to your ec2 instance (You can have any combination of gp2 or hdd EBS volumes, they just need to be &lt;= 30gb)
Did you allocate more than 20gb for your RDS instance
Have you been stopping and starting your ec2 instance multiple times an hour (Each time you stop then start your instance the clock starts over on the running costs. Restarts keep the clock running)
Multiple snapshots of the EBS/RDS volumes