Placing a rally banner inside the Arena makes it unusable
Shame http://brightrockgames.userecho.com/topics/1269-you-can-place-a-rally-banner-inside-the-prison/ got closed, as it also can suffer. If you place one inside the Arena, all units inside will be pushed out. Additionally, you can't place any unit inside while the banner is there. It can cause a good grief if an enemy unit escapes thanks to a mishap with a banner.
In version 1.5 Rally flags can not be placed into Prison nor Arena anymore as well the Shockwave spell wont hit units behind walls, obstacles or inside Prison/Arena.