I know about user agent stylesheet but I am seeing user stylesheet only on some specific sites in the Styles section of the developer tools, even though there is no Custom.css in my User Stylesheets in my Chrome Profile.
These "User stylesheet"s are added by Chrome extensions, either declared in a manifest file, or using chrome.tabs.insertCSS.
Styles on the web page always take precedence over the user stylesheet, unless the rule set in the (extension's) user stylesheet has a higher specifity.
If you want to know which extension is responsible for these stylesheets, just disable the extensions one by one until the stylesheet goes away. After disabling an extension, select a different element in the inspector, then select the original element to refresh the view, you don't have to reload the page.