The message seems more that they outgrew AWS lambda but that lambda was a good choice at first.
Emphasis on "their server less architecture". Sometimes good tools are used poorly.
For example they describe a high throughout workload, and each workload spread through a bunch of lambdas that handled bite size bits of the workflow. Also, they managed the workflow with step functions. Just imagine the number of network calls involved to run a single job, let alone all the work pulling data to/from a data store like S3 into/out of a lambda. I'd guess the bulk of their wall time was IO to setup the computation.
Of course you get far better performance if you get rid of all these interfaces.
“There are use cases where Amazon EC2 and Amazon ECS are a better platform than AWS Lambda” is…not actually a message that anyone involved in AWS has ever been afraid to put forward.
I mean, the whole reason that AWS has a whole raft of different compute solutions is that, notionally, removing any one would make the offering less fit for some use case.
The article mostly lays the blame on step functions. Also, lambdas are portrayed as event handlers that don't run relatively often. This means long running tasks that are ran occasionally, or events that don't fire that often. Once throughout needs go up or your invocation frequency comes closer to the millisecond then the rule of thumb is that you are already requiring a dedicated service.