Strange Keychain Popups in Safari
Open Keychain Access.app in your Applications > Utilities folder. 
Highlight the login keychain on the left sidebar.
Select one of the sites you see the popup from the list of credentials and double-click to get the info panel.
On that panel select "Access Control".
Below "Always allow access by these applications" click on +, and navigate to Safari in your Applications folder. Save changes.
Close Keychain Access and restart Safari.


(adapted from this answer. You may need to do steps 3-5 for each site for which that problem is occurring; I'm not certain.)