Stacking order when you have multiple modal dialogs and popovers in the top layer is based on most recently revealed element, so that toast that just opened is now hidden under a dialog. Anchoring is currently only supported in Chrome, so popover tooltips show up in the corner. Firefox supports transition animations when opening a dialog but not closing it. The web platform feature needed to tie the mobile back button to closing a dialog isn't actually implemented yet. Frameworks that patch the DOM might clobber modal dialog state because it's a function of both the "open" attribute and the result of showModal().
Some of these will improve but I think the display order problem is here for the long haul.