Why some iphone apps won't finish ssl handshake with Charles Proxy?
Yes, SSL pinning is a possibility. Although as of iOS 10.3, you must take an additional step to trust the Charles Root Certificate that is not currently documented on their website edit: this info is now under iOS Devices here: https://www.charlesproxy.com/documentation/using-charles/ssl-certificates/
Settings > General > About > Certificate Trust TestingsSource: https://www.neglectedpotential.com/2017/04/trusting-custom-root-certificates-on-ios-10-3/
There are applications which don't simply expect the certificate signed one of the trusted CA's on the system, but which expect a single specific certificate or a certificate containing a specific public key. This is called certificate/public key pinning. For this application it will not work if you configure the CA of Charles Proxy as trusted on the system because they will not use this CA.
Any explanation of this/way to fix it?
If the application is built to only trust a single certificate/public key and never trust something just because it is signed by a locally trusted CA, then you would need the original certificate and its private key to do the SSL interception. Since you don't have these there is no way to do the SSL interception.