Zoning and MM pets
It has happened for me as well, although it is some time since last.
If it happens, I just continue to do what I intended.
Usually after a while they will get back under my command.
It is said that buffing the pets, often can bring them back as well.
For me at least, if I zone into a mission, they will be back under my command.
It's been this way for a while now. Target the pet that is no longer under your control and hit it with a buff of some kind. Something like a single target heal, or whatever. If you are a pure debuff set if you target it with an upgrade it should come under your control again.
Unless you are encountering a different bug?
If it's the bug I'm experiencing, it's different. Pets stay in the window, but can't be controlled, dismissed or anything, and refuse to move from the zone in point.
Several times now when I've zoned from one city zone to another with my mastermind pets out, I get a bug where my pets stop responding to any commands, including the dismiss command. If I go through a door or zone again they will appear next to me, but they will not follow, fight, dismiss, or obey any commands whatsoever. So far the only fix I've found is to log out for a sufficient amount of time, which needless to say is very annoying. In fact, the reason I'm on the forums right now is because I'm waiting for my MM to reset while logged out so I can play him again.
Anyways, I checked the first couple of pages here and haven't found anyone mentioning this bug. If any of you have seen this bug as well, it might help the devs see the seriousness of the problem if more people mention it.