When programmatically creating visualizations with two or more tables, it can be that the specified ColumnRelation(s) are enough to properly link the data but that not all columns involved in the visual are matched, i.e. the visual and tables are properly configured.
However, Spotfire will show a warning message in the visual about potential mismatches. As the message indicates, this be a problem (or not). The Spotfire tool provides a checkbox in the visualization configuration "Show notifications about mismatches" that allows this warning to be shown or hidden.
However, there is no public API to do this programmatically.
The suggestion in this case would be to include such functionality in the Spotfire Analyst API.