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When EC2 instance and S3 bucket are in the same region - customer needs to ensure they use VPC Gateway Endpoint for communication between the two. If VPC endpoint is not used - this will likely fall under the Regional (Inter-AZ) data transfer category. That's exactly what "EU-DataTransfer-Regional-Bytes" usage type tells us.
Note that the charge should not be on the S3 side, but you should see it linked to EC2, as the instance will be communicating with S3 via public endpoint / public IP address.
More info in the blogpost about VPC endpoints: https://aws.amazon.com/blogs/aws/new-vpc-endpoint-for-amazon-s3/
And documentation: https://docs.aws.amazon.com/vpc/latest/userguide/vpc-endpoints.html
Check out EC2 pricing for more info about Data Transfer here (specifically section around Regional Data Transfer charges): https://aws.amazon.com/ec2/pricing/on-demand/
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