This isn't necessarily about the selected website in question, but it is about the 'My Websites' dashboard here at wpmudev.org.
I had two plugin updates available, when updating the first something went wrong and the update failed (it is still at the older version). Then I updated the second plugin and it succeed at updating the second. But the dashboard now shows that both plugins are up-to-date despite the fact that only one should be.
The issue preventing the update of the first plugin is file/folder permissions (the file owner is not the same as the web process). But regardless of the source of the failure the dashboard should still report one update available, imo.