The battle bug went away when I log on the next day but to explain more on on it; whenever I would enter a battle, I would be unable to click any of the 4 options (fight, Pokemon, items, run away) with my mouse or the shortcut hotkeys resulting in I forcing to log out of the game. This situation arose only after that rare encounter icon appeared.
From what I have experienced, the rare encounter icon displays during a battle but this time the icon displayed after I had reconnected back into the game and was relocated in the most recently visited pc.
Hopefully is was well explained enough for it to be understandable. Regarding the shiny Pokemon encounter, I understand and thank you for the reply.