The formatting icons of the VisualEditor toolbar are currently "B" for bold, "I" for italics, the chain for links and the remove icon to clear formatting.
This series of icon seems to indicate that links are a kind of formatting. However; "Clear formatting" doesn't affect links; it only removes bold and italics.
Either links *are* a kind of formatting, and the "Clear formatting" action should remove them, or they aren't, and the Link icon shouldn't stand in the middle of icons that add and clear formatting. The current order and behavior are confusing.