So basically the bot won't requeue if i manually leave the battleground while the bot is still running. I will get deserter then it won't requeue once it wears off. any way I can get it to do that?

Just use the Stop key bindings really fast. Alt+C. Then Hit the same Keys again to restart the bot. This will fix that for you. But I do think that if would a good idea to have the bot monitor the Cooldown on BG or Dungeon Deserter.

I typically do that but when i'm not monitoring it and this happens it's really unfortunate because then it just stays logged in and looks suspicious because i'm just standing there not doing anything.

Hello,

 

It is not normal.

 

I have fixed problem, wait next update thank for repport.