One of the most common causes of heating is high power usage from the battery (where it's the battery that's heating up). One of the most common battery drainers are the screen, the camera and the antennas (more specifically, the one for mobile data). Video chat uses all of these three phone components. However, you may still be able to minimize the heating by:
1. connecting to Wi-Fi instead of Mobile data, and then ensure that your Wi-Fi signal is "strong";
2. use a lower screen brightness during the video call;
3. keep the back of the phone ventilated during the call, i.e. do not lay it flat on a surface or enclosed in a phone case.
Generally, some amount of heating is acceptable, but something that heats up beyond 42 degrees Celsius is unsafe for any portion of the human body. There's no need, however, to measure if it's exactly 42 degrees already - if it's painfully hot, then it's harmful. Heating will also be harmful to the battery of the device, shortening it's usable life. There have also been incidents of exploding rechargeable batteries in much older devices... though that's unlikely to happen with our more modern Windows Phones. Therefore, some heating is safe, but over heating is not safe.