User blog comment:USARMP/Cerberus Equipment/@comment-5379655-20130106030039

Honestly, it's probably just design oversight or artistic license. In real life, insignia's and color schemes would be altered to match new allegiances, similar to the Normandy's new paint job in ME3. The military is a stickler for things like that. However, it wouldn't really be identifiable as Cerberus (especially the armor) without the symbol or paint job, so Bioware most likely took artistic license with it.