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Hard to answer without digging a lot - Are you sure the lambda is only executing once...its also possible some part of your code is making two calls (but only logging once)
Using lambda to start fargate tasks to process files in s3 is not a great pattern as error handling etc is difficult and I would suggest using step functions which can be triggered via event bridge and can synchronously start fargate tasks and have all the required logic/error handling
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Switched to using event bridge and step functions and that worked much better. Thanks.