File menu > compact.

I get this problem too, quite often actually, about every other day. The emails appear in one of two ways, from what I have noticed.

1. Arrive with the new mail fetch during start-up. That suggests a possible error during the email sync.

2. Appear as the result of a "delete" action, either an email in the inbox, or an RSS feed entry.

These emails appear to be only part of the Unified Inbox, they cannot be seen in any specific email address inbox. This can be seen in the screen-shot, the Unified Inbox reports 8 emails, but the individual Inboxes only report 5 and 2 respectfully; 1 short, the blank one with the Epoch (?) date.

Opening the blank email to read, I have found that it shows an email that had been in the Inbox previously, but had been deleted. In my case, this was from the day prior.

It has been suggested that menu option File / Compact will remove them, but no, at least not that straight forward. File / Compact will often remove them, but not always, after they have been "deleted" and return back to the Unified Inbox as a "read" item.

The problem with attempting to "delete" them is, they are not really there. If one attempts to delete these email, an adjacent email in the inbox gets deleted instead, and the blank one just sits there waiting still.

To delete the email, without deleting any other emails, all other emails have to be removed from the Unified Inbox. This, I can manage, as I regularly keep my Inboxes empty, but if one had hundreds or thousands, that might be a little more troublesome. And if one had that many emails, any blank ones may well be at the bottom of the Inbox, as the oldest, and out of sight most of the time.

… an unusual application feature :) but must be related to the background database system.