I don’t know if this is an issue with Skype or MCC, but whenever I get a call on Skype, Halo MCC would automatically minimize and act like it isn’t running even though I could hear the in-game audio. I can’t even bring the window back up because the application would just disappear on the shortcut tab. Only thing I could do is to force shutdown via Steam. I have been able to consistently reproduce this issue with a friend. Is this a bug with Skype or Halo MCC because I am worried that this would end up counting as if I am leaving matches and I don’t want to get a penalty for the first time because of a bug like this.
There is a current known issue where Alt + Tabbing can cause the game to vanish. What you are experiencing sounds a bit similar so I’m thinking Skype may be doing something in the background similar to an Alt + Tab function. I dug up a waypoint thread with some community members posting various troubleshooting steps. Give the thread a lookover and let us know if any of those steps help!
Also, to ease any concerns about penalties, there is an automated system in place that penalizes players who quit out of matches. The punishments from this automated system are not severe as it only prevents you from playing for 1-10 minutes depending on how often you quit during a certain time period so as long as it is truly accidental and out of your control I wouldn’t worry about it affecting you.
If any of the steps in that thread help, it would be beneficial for the developers to know what fixed it. I would encourage submitting a ticket over on the support site letting them know what fixed the issue for you. If the steps do not help, definitely submit a ticket as the developers will be able to help you dig deeper into resolving this!