When changing filters at the page/folder level, every element on the page has the filter applied to it, including linked charts. However, since filters don't apply to linked charts, the viz gets a warning message that the filter doesn't apply to the viz.

It would be fantastic if the page/folder level filter changes did not apply to the linked visualizations.

For clarity, this is referring to visualizations created by first selecting a table and then selecting the visualization using the icon at the top of the page which results in having both the table and the visualization on the page.