When you clean a project, you actually clean only main target. If you want to clean all targets, for example, Pods after installing new versions of pods, you should use another option.

To clean all targets in XCode 6 including Pods use Shift+Cmd+Alt+K button. It calls “Clean Build Folder…” command, which is not visible from menus.

Probably, I don’t know something, because this way of cleaning seems to be not so obvious.