In general, iPhone prioritizes voice (GSM) calls over data traffic, and VoIP calls such as the ones made using 3CXPhone are perceived as data traffic. The following scenarios have been observed when a GSM call and a VoIP call (on 3CXPhone for iPhone) occur at the same time on an iPhone.
If during a VoIP call, a Voice (GSM) call is received, it will be given priority over the VoIP call. The call on 3CXPhone for iPhone will be placed on hold for the duration of the GSM call. The VoIP call is automatically re-established when the Voice (GSM) call is disconnected.
On the other hand, if during a Voice (GSM) call, an incoming VoIP call is attempted, the VoIP call will be ignored. The VoIP call will behave as if the call was not answered.
This is not a bug with 3CXPhone for iPhone, but rather is the way that iPhones have been developed, which in turn effects VoIP calls made using 3CXPhone for iPhone.