We don't normally use CT raid tracker for monitoring bosses, but we've noticed that the addon hasn't been detecting the later bosses in the instance (AQ40). Instead, all loot that has been dropping has been getting assigned to "trash" instead of the bosses.
More of an annoyance than an issue for us, but thought I'd mention it in case any guilds were using the boss kill tracking.
Were the loot targets within range when you gave them the item? If they are far enough away, the item will not be shown in your loot log and that is how the addon can track who gets what. Let me know if you think this was involved for your report. Otherwise, I'm going to see what I can figure out with my next AQ runs.