First I had a cluster with one node. I've increased one instance(node) so now it should show that I have 2 nodes but instead it says I have 3. Why is this?
That will be temporarily since AWS follows blue/green deployment model. Please see this link.
When you have a cluster with 1 node and add 1 more node, AWS ES will create a new cluster with 2 nodes and then copy the entire data set from older cluster to new one. While the copying / migration operation is in progress, you'll see 3 nodes - 2 from new cluster and 1 from old cluster. Once migration is completed, the node belonging to older cluster is deleted.