Is there a way to flag a task in project that has passed its end date but is not yet complete? I can change background color of the task name to identify it that was but am wondering is there is a way for the tool to do something automatically.

I'm guessing you mean past its baseline finish? You could certainly apply a highlight filter looking for tasks with finish variance (assuming you have saved a baseline) that have % complete < 100%.

Another option is to use the Status Indicators. While they won't change background color, they will flag tasks that are late.