We're getting roughly one "$workflow is not UUID or Workflow instance" exception a day in production from includes/UrlGenerator.php, triggered either from a notification API query or Special:Notifications.
BasicFormatter is passing a NULL workflow to generateUrlData(), so I guess the event object's getExtra() didn't contain the expected 'topic-workflow' key, or it was null.
It might be worth catching the exception, logging it in a Flow file, and returning a dummy formatter rather than aborting the other user notifications. (If that's what's happening.)
Here's one of the exceptions from the notification API query. You have to be logged in, and if I paste the URL it seems to work, so to reproduce we'd have to try to find the user(s) with the troublesome notifications. I wonder if it could be notifications regarding a deleted or suppressed workflow.
2014-03-03 19:26:00 mw1145 enwiki: [5c973112] /w/api.php?action=query&format=json&meta=notifications¬format=flyout¬limit=7¬prop=index%7Clist%7Ccount&_=1393874759279 Exception from line 144 of /usr/local/apache/common-local/php-1.23wmf15/extensions/Flow/includes/UrlGenerator.php: $workflow is not UUID or Workflow instance
#0 /usr/local/apache/common-local/php-1.23wmf15/extensions/Flow/includes/Notifications/Formatter.php(39): Flow\UrlGenerator->generateUrlData(NULL, 'view')
#1 /usr/local/apache/common-local/php-1.23wmf15/extensions/Echo/formatters/BasicFormatter.php(647): Flow\NotificationFormatter->processParam(Object(EchoEvent), 'post-permalink', Object(Message), Object(User))
#2 /usr/local/apache/common-local/php-1.23wmf15/extensions/Echo/formatters/BasicFormatter.php(361): EchoBasicFormatter->processParams(Array, Object(EchoEvent), Object(Message), Object(User))
#3 /usr/local/apache/common-local/php-1.23wmf15/extensions/Echo/formatters/BasicFormatter.php(260): EchoBasicFormatter->formatFragment(Array, Object(EchoEvent), Object(User))
#4 /usr/local/apache/common-local/php-1.23wmf15/extensions/Echo/formatters/BasicFormatter.php(222): EchoBasicFormatter->formatNotificationTitle(Object(EchoEvent), Object(User))
#5 /usr/local/apache/common-local/php-1.23wmf15/extensions/Echo/controller/NotificationController.php(338): EchoBasicFormatter->format(Object(EchoEvent), Object(User), 'web')
#6 /usr/local/apache/common-local/php-1.23wmf15/extensions/Echo/api/ApiEchoNotifications.php(144): EchoNotificationController::formatNotification(Object(EchoEvent), Object(User), 'flyout')
#7 /usr/local/apache/common-local/php-1.23wmf15/extensions/Echo/api/ApiEchoNotifications.php(26): ApiEchoNotifications::getNotifications(Object(User), 'flyout', 8, NULL)
#8 /usr/local/apache/common-local/php-1.23wmf15/includes/api/ApiQuery.php(279): ApiEchoNotifications->execute()
#9 /usr/local/apache/common-local/php-1.23wmf15/includes/api/ApiMain.php(861): ApiQuery->execute()
#10 /usr/local/apache/common-local/php-1.23wmf15/includes/api/ApiMain.php(362): ApiMain->executeAction()
#11 /usr/local/apache/common-local/php-1.23wmf15/includes/api/ApiMain.php(333): ApiMain->executeActionWithErrorHandling()
#12 /usr/local/apache/common-local/php-1.23wmf15/api.php(76): ApiMain->execute()
#13 /usr/local/apache/common-local/w/api.php(3): require('/usr/local/apac...')
#14 {main}
Version: master
Severity: normal