I KNOW WHAT THIS IS... I think :P
In that particular mission (Clear Tv...something), those Missiles you are talking about are always there, HOWEVER they are only used on certain events.. The mission is.. dynamic in a way, for example: Once you will receive a message from the tower that the enemy has placed a HAWK battery in the area, destroy this then continue with planned mission. THESE are the missiles you are shooting. When any of the other events happen (nothing, and I've also had the tower say that there is incoming aircrafts, return to about 500m from the FARP and wait until Dandra I think it is sends some MIG's to take them out. Another event is when some planes come in and carpet bomb the area for you.)
So, with that particular mission, IGNORE the missiles unless you get the message, in which case they should attack you.. They are arranged in a cube configuration, one pointing each direction right?
Hope this helps.