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Things I have noticed if I have 2 or more AAM Cannons at the same time.
1: On occasion, only 1 will fire missiles, the others do not fire at all.
1A: Only 1 will fire missiles, but it fires more often, as if one or more of the others are still working, but all launching from a AAM Cannon.
2: On occasion, a missile deployed by the first stage will go after either another AAM Cannon, or the AAM Cannon that launched the first stage in the first place.
3: Relating to 1, 1A and 2, many/all of the AAM Cannons suddenly fire normally, but most of the missiles go after the AAM Cannon that launched them or adjacent AAM Cannons, usually taking out all but one of the launcers, with the one that was firing normally all along being the usual survivor.

The AAM Cannons were on the ground during these incidents, the hit AAM Cannons were the only things in the missile's path. At least one instance saw missiles making an active attemp to seek an AAM Cannon right next to the launching AAM Cannon, the missile had to make a sort of ? shaped path to hit, so it was obviously targeting the adjacent AAM Cannon.
These 'friendly fire' instances seem to mainly occur when there are no enemy craft on the map, including 3.
Another instance had a potential friendly fire incident, but an enemy craft appeared as a missile was halfway back down to an AAM Cannon, and it turned to go after the newly arrived enemy craft that was some 2 screens worth away.
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Yes, the lua-part of this mod is really wonky and hard to realize with CC-Lua.
Problem is that I have to "transfer" the team-variable from first stage to the actual missile. I have to use a global variable being set to the team-number as the first stage explodes, then have second stage set self.team to this variable and then set the variable back to nil again, all within 2 lua-updates. It's something I really don't like, and why I decided to stop working on this mod for now..

It's probably best to stuff it all in Cannon.lua, because the launcher has to first find the target anyway before launching missile, so then the missile doesn't have to find it again. And the next stage depends on the previous stage, so it makes sense IMO. You also wouldn't need to worry about passing variables around.