If I assume that you are Inputting from a database and asked to see the process, then the warning indicates that because of either the embedded SQL in the Input widget or your database access is not allowing Alteryx to show that progress. I get that message occasionally when I access Teradata via Views in my Input widget. This will not affect the workflow, only the visualizations.
as with most warnings, once you've verified they are not impacting your workflow; you simply ignore them. the visualization that I referenced is in during runtime you see a percent complete cycling above the input widget. And the option to choose in your input configuration is "Do Not Show % Complete".