The Problem: I have discovered that you can immediately make a couple of scout planes and fly them over the enemy. Then everyones commander will stop what they are doing fire at your scout planes. If you have enough of them which is really easy to do all enemy commanders will not be able manufacture anything. This can be used to buy enough time to make offensive units and destroy all the commanders. This is a glitch that can immediately end a match within minutes. TL;DR:Scout planes can be used to immobilize the enemy and kill within minutes, with no fight back The Solution:Make it so your commander does not automatically fire at enemies, so you can break the cycle of shooting at a plane to fast to hit.
Solution #2: While the other guy is spending metal and energy making hordes of harmless scout planes, spend your metal and energy making tanks. Problem solved.
It sounds like an AI glitch to me. Whiffing into the sky is a natural part of the game of course, but not to the detriment of a unit's given orders.
You guys do know that the Commander keeps building while he's firing, right? If you just leave him there he will build and fire at the same time. The nanolathe FX aren't emitted, but he's still chugging away. This is a separate issue in itself, though it has already been reported in the bug tracker.
As said, the commander doesn't stop building although graphically it looks like this. Just build a single AA tower and the problem is solved and you'll have a nice shower of scout debris.