After getting Tableau Prep to work on a different Mac, the only difference I noticed was that for some reason the My Tableau Prep Repository folder on the mac with the System Error was located in my iCloud/Documents directory. I used File->Repository Location... in Tableau Prep to change the location to a folder on my local drive. Prep restarted and now everything seems to work.
I just upgraded to 2018.3.1 and I am having this same issue with the same system error code in the screenshot provided by Todd. I can't even connect to any files and can't even begin any flows or open flows created in the older versions of prep. very frustrating
I'm having this issue too. It happens while connecting to PostgreSQL. It's impossible to get anything done. I'm working with Prep 2018.2.3. Prep says:
com.tableau.loom.exceptions.InputNodeFailureException: Eingabeknoten kann nicht ausgeführt werden: Failure loading Data Source: Invalid input: mismatched brackets