This one has been around for a while but only now more relevant with the restoration of label filtering in email.
If you have 2 email panes (say, with 2 different filters of your inbox) and open an email from 1 pane then click (or double-click) on an email in the second pane, the Gmail message pane correctly moves adjacent to the second pane but after loading Gmail, shows the message that was selected in the first pane. If you click on another message in the second email pane, it displays that message properly in the Gmail message pane. This also happens when opening a message in the Outline when a Gmail message pane is already open. If you close the Gmail message pane, before opening the next message, this doesn’t happen.
This also brings to mind one other thing we discussed in the past. Would it be possible to, instead of reloading Gmail whenever selecting a message from a different pane, reuse the already open (or previously opened) Gmail pane, so move that pane when selecting a message from a different pane? And ideally, when closing a Gmail message pane, hide it to allow it to be reused later, whether a message is selected in the same pane or another? This would save the constant reloading of Gmail.