@ GamerGD3:
What platform are you playing on?
On Android, I can tap on ghosts that aren't auto-collected, go back to my Springfield and I get credit for GOO that wasn't explicitly collected by me or the automatically.
As far as the black dialogue box, if you don't haunt the 3rd building, that box will never appear. In other words if you haunt 2 buildings and tap 5 ghosts, then that box won't appear. It is either triggered when you haunt the 3rd building and collect the GOO that was dropped from all 3 hauntings or the game auto collects it. Either way, after the box pops up you can still tap ghosts until you reach the standard max of 5. Before the update was patched, you could tap 4 ghosts and then quickly tap 3 or 4 ghosts in close proximity and get more than 5 ghosts in addition to the 3 hauntings.
My advice is to max out your friends and visit all 100 daily, drop gremlins and keep at it. I've accumulated close to 32000 GOO as we speak.
