Red-eyed 'Impostor' Agents appeared at the start of The Matrix Online storyline during chapter 1.1. These 'Agents' impersonated system representatives and began widespread sabotage and assaults on the awakened redpills in an attempt to stress/break the truce agreement. All three major organizations (Zion, the Machines, and the Merovingian) were quick to deny being responsible for the attacks and the impostors were soon declared a fourth group unto themselves.
It was soon discovered that these beings were not Agents at all, but rather were using some kind of disguise technology to try and implicate the Machines for their actions. Glowing red eyes and lack of system-issue firearms were flaws in the plan.
It is revealed in a "Report to the General" document that the Red-Eyed Agents are the General's (the Exile who used to command the Sentinels) commandos, taking into consideration that programs could gain access to other shells (like the way the Oracle changed appearance between Reloaded and Revolutions), made occasional documented reports to the General in various Zion and Machine critical missions, and also hinted that their disguises were malfunctioning.