I've noticed this with WhatsApp. Upon replying to a message notification directly from the notification pull down (or from the heads-up pop-up), the original notification sticks around and the newly sent message gets added to it. In other words, I receive a message on WhatsApp. The pop-up shows me the preview. I pull down the notification drawer, expand the notification and click on Reply, type in my message and hit the Send button. My new message gets added to the old notification (as if it were the WhatsApp chat view) and remains in the drawer. The icon in the notification bar stays too, and if the screen is turned off, the notification LED starts to blink as if I have yet to read the notification.
As far as I know, this isn't normal Android behaviour (where the original notification is automatically dismissed after the reply is sent/the action button is pressed).
The first notification behavior that you commented on is by design. It's how Whatsapp intended it to work. I just duplicated the behavior with another brand. The blinking LED notification is however not by design. This is a BUG that I will report to our devs. Thanks!