Inconsistend behaviour with custom script at linux

I am executing a custom script on an azure Linux machine, the custom script is referring to a shell script which has few long-running commands.

I have observed intermittently different behaviors with the output of the command
- Sometimes the long-running command is getting terminated in between without any error.
- Sometimes command failed with error:
`cannot touch '/etc//repl-force-mysql': Read-only file system`

Though, If I execute the same shell script on the terminal of the same machine after login via SSH script is succeeding.

- /var/log/azure/custom-script/handler.log
- /var/log/waagent.log

I didn't see any error in the above-mentioned logs. Please share email Id where I can share these logs.