Are you saying putting on and taking off a case may cause a phone to bend? I could understand that sitting on a phone could bend a phone but not putting in a case. If putting on a case on can bend an iPhone, then the iPhone 6/6+ are the biggest piece of garbage phones in the world.
It might not be visible now but will become more visible with each passing week. The integrity of the unibody has been compromised and will bend more and more.
No, I'm saying that wrestling with a case constantly could possibly cause an issue with the way the glass sits. Some of the cases are extremely tight and I've actually had to give someone at Apple to help me remove them in the past.
If not that, then something caused this phone to no longer meet the OP's standards. He can't see any bend at all - so that would suggest a warp somewhere.
Or a wrap, if you prefer.