Commando with 3 specialization points should award 9 AP after killing an enemy with a burst. This is what usually happens, but there's a few weird interactions with other AP sources that make it award less AP or even take AP away from the player. There's only two that I was able to find out and reproduce without fail:
1. If the weapon has a rapid reloader, triggering its AP bonus within the same burst as commando (but before commando, not after it) causes commando to award only (burst AP cost - rapid reloader AP bonus). Example:
The player has an SMG that has a base AP cost of 8 with the rapid reloader equipped. 7 after the DEX reduction. This means their burst AP cost mentioned above is 14.
The SMG also has a 25% chance of giving the player 4 to 8 AP on each shot.
The player uses their 9-shot burst, the rapid reloader gives them, say, 6 AP on the 2nd shot. The enemy is killed on the 6th. The player should be awared 9 AP regardless of what the rapid reloader gave them - but, because of the bug, will only get 8 AP instead, because 14-6=8.
Picture of this actually happening in-game:
https://i.imgur.com/n4uOBBQ.pngNote: This would not happen if the 6th shot killed the enemy, but one of the remaining 3 shots triggered the rapid reloader AP bonus after the kill. In that case, 9 and 6 AP would be awarded.
2. The same will happen if one gets the rapid reloader refund with a sniper rifle (or by using Dragunov) while having the shooting spree active. Since the rapid reloader bonus can easily get over the burst cost of an SMG, this can result in negative AP "bonus" from commando. Example:
The player has the same SMG equipped, but also the Dragunov in the other hand. The player activates Shooting Spree, uses Aimed Shot with the Dragunov, kill the enemy - 30 AP is refunded by Shooting Spree, 15 from rapid reloader. The player then switches to the SMG and gets a kill with one burst - since 15 AP is more than the 14 AP required to burst, the player is awarded -1 AP, which does in fact reduce his total AP by 1.
Picture:
https://i.imgur.com/TSikaRg.pngNote: This doesn't happen without shooting spree active. No idea why.