I have noticed that when running from a long distance when right clicked on an area of the map then clicking again in the same area but on a creep, every once and awhile my hero will stop walking.. Don't know if it is happening to everything else..

Yes the reason for this is because you went to attack a creep, because the creep had died after the click, your hero stops because there is no creep to attack. This is why they added the hotkey X to attack an area. Hope this helps.