I am seeing the same symptoms on the FPM and FPM-ALPINE 16.04 Docker images. Have tried increasing PHP timeout and memory limit values. Also, the web app shows: Error when assembling chunks, status code 504 similarly to what has been reported here: Error when assembling chunks, status code 504). The worst part is when the upload fails, the chunks that are written are not removed therefore we have a number of large partial uploads without a great way to purge them.
If I switch to local storage, I still get the 504 error but the files at least upload. Would prefer S3 though.
Similar issue has also been reported here: https://github.com/nextcloud/server/issues/7919