I haven't seen Tableau behaving that way and I would probably start troubleshooting issue by checking for any filters defined on the Data Source that might be restricting the data from being visible.
What is the total count of records displayed after extract refresh?
Did you try troubleshooting issue by running refresh on Desktop?
It is a known issue that incremental refresh may not work for published data source with data source filter. Not sure if this is what you went to.
I'm currently running v 10.5.1 so hoping an upgrade will resolve this as i've seen in 2018.1 release notes:
Views did not update with new data after performing an incremental extract refresh in Tableau Desktop