UPDATED 6/8/15 : Google informs us that the fix for the reappearing trash rolled out over the weekend, so the issue should be resolved.
[UPDATE 5/26/15 8:45A] :: Google says they've found a bug for the reoccuring trash problem, and are working on a fix now. There is no announced timeline for when the fix will be implemented.
Google has changed the way deleted and archived mail work and this has caused some users to see email that had been previously deleted return to the Trash folder. Google Apps accounts have unlimited storage, so any additional email will not affect your ability to send and receive email. Trash and Spam folders will automatically delete messages when they are no longer accesible through historical archives. This feature was designed to better enable users to recover deleted messages which may have been deleted in error, however we are in contact with Google to investigate the specifics of this issue.