So i was playing and got afk'd out of the bg by being reported and couldn't get in combat in time does this flag my account or anything am i fine to bot?
some players prob. just reported you as AFK because you were standing arround in other words - go and hit that start button.
I wouldn't worry about being reported AFK in a BG, unless it happens over and over again. I mean we've all had real life things come up where we just had to leave the computer. A single report shouldn't be an issue. Getting afk flagged 20 times a day probably would merit some sort of investigation I would think.