[kitten320]

Mai HiME since Madoka technically borrowed a lot from this show. Girls with special powers are told that they need to protect humanity from monsters but is that true?

Attack on Titan - anime does not go that far just yet but with recent manga chapter releases it is similar to what you are looking for.

D.Gray Man - it's long running shounen series but further it goes the more you start to doubt the good cast and especially their higher ups.

Fate/Zero - not exactly but it is believed that whoever wins Holy Grail, will have their wishes fulfilled. Is that so though?

Not exactly either but original FMA anime could work to an extend since creation of homunculus, the main villains is very different from Brotherhood.

I also second Ga-Rei Zero.

Psycho-Pass - you have this new, amazing system that cat detect criminals before they commit a crime. But how flowed is it and how exactly does it work? What stands behind it's creation? That's what main cast of police is to discover. Their government is not as flawless and amazing as they think.

Shiki - not really what you want but it focuses on morale and who is a real monster. Friends fighting friends.

Shinsekai yori - I can't remember the details but government was deceiving and lying and lots of dark and twisted stuff was done behind peoples backs.

Zetsuen no Tempest - a girl is murdered and two friends try to learn the truth. But the more they learn the less it looks like a casual murder. Just what exactly happened and did they know her as well as they thought?

Kamisama no Inai Nichiyoubi - several arcs and each one has a secret for you to learn.