I don't know. You may want to submit a Tableau Support ticket for help on this. They will want to see your log files.
Does the refresh work on the same version of Tableau Desktop as your Server? If so, try republishing (from Desktop and not TabCMD/REST API)
I've had similar errors a few times with extracts created via Extract API and published via TabCMD - re-publishing via Desktop fixed them. But with these sort of errors you're basically looking at a black box, so you'll want to engage Support if you want to get it resolved permanently.
I just had this issue today
com.tableausoftware.nativeapi.dll.LogicException: LogicAssert at d:\tc\builds\tableau-9-2\tableau-9-2.16.0204.1543\modules\server\tabsrv\main\server\VQLServer.cpp line 359: false
I use version 9.1.1 found the same error about "...Logic Assert ... WindowCollection.cpp " when extract refresh and fixed.
You can try solution as below...
On Tableau Desktop
1. Check the worksheet filter
- Drag on "Apply to Worksheets"
- Choose "Selected Worksheets..."
I found error "Internal Error - An unexpected error occurred and the operation could not be completed."
2. Fix "Internal Error" as link (Option 2) : Error "Internal Error - An unexpected error occurred and the operation could not be completed." Filtering Selected Sheet…
3. Re-Deploy workbook.
4. Test refresh extract on Server.