FALSE ALARM!
I figured it out. I had some SP-SAM units I had set the range to 0 and hid out of the way in the woods while I was running different tests. It seems they must have ben emitting their radars as the planes were occasionally trying to take them out. Since I had the flags off and the planes didn't kill the SAM's there were no extra explosions. Without the flags I didn't see them hidden in the woods.
I ran some other tests with a fresh scenario and things seem ed to work really well. I did notice that planes occasionally targeted the SP-SAM's this time BUT at least now I know what they were off chasing. These were fighter-bombers aremd with missiles, not bombers. The bombers went straight for the original targets.