Earlier quoted context omitted.
This must be a regression bug in AWS's internal system. At a past job (2020) we used S3 to store a large amount of genomic data, and a web application read range requests to visualize tiny segments of the genetic sequence in relevant genes - like 5kb out of 50GB. If AWS had billed the cost of an entire genome/exome every time we did that, we would have noticed. I monitored costs pretty closely, S3 was never a problem…
S3 egress costs are free if the traffic stays within AWS. Sounds like your clients were EC2 instances so this wouldn't apply to you, would it?
Not if it's cross-region.