i saw this too and made some tests -
one reason for this annoyance is that if you delete an unread message from your pc account, while there are other unread messages, a false mail notification will appear in the android device. this is clearly a bug. i made many tests and this is proven. (i use the native gmail app)
however other people here claim they do not touch the pc, so clearly this is not the only case when this happens. maybe an email going to the spam directory cause that?