As a mining mission completes the message " press "b" to continue " pops up on the hud just under the distance meter for a few seconds or so as the ship continues to mine.

No real issue, just thought I'd flag it in case it is meant to pop up under different circumstances.

I assume this is PC? Is it Windows?

So, it is likely that you have a joystick or gamepad set up, which is causing the mission to suggest you hit "B" to use Activate to complete the given objective.

So.. this is probably behaving as expected.