Schedule refresh says complete but partial data shows up.

The semantic model refresh has no idea what you mean by "partial data".  All it does is run the mashup queries, with whatever data is available.  You may have a timing conflict when the refresh happens before the source system is updated, or some timezone timing issues, or any other reason. 

Ideally you would abandon the scheduled refreshes and instead base your refresh request on a signal from the data source that it has completed its own refresh.  You can do that with Power Automate, for example.