To allow/disallow the clearing of warnings or dismissing of errors you can check these permission boxes appropriately on the Role Management tab for a particular role,

If you give some of your agencies the power to clear their own warnings you can see which ones they have cleared by going to the Errors and Warnings page, selecting the 'Display with the latest explanation.....' checkbox is shown in the screenshot below, and selecting 'Warning' and 'Dismissed/Cleared' from the Type and Status filters.