Zombie Pets and Trams
I've had various pets do that, on and off, entering or exiting misisons - can't even get them to dismiss at times.
I've sent a bug report about it. Seems like zoning most any way, even into missions, causes them to stick.
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If you're describing what I think you're describing, buffing the pet should get them to obey you again (I forget if the upgrades work for this or if it's just regular buffs). I had to do this quite a bit on my Necro/Therm MM when the zoning pets feature first went live.
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the most simple fix for this right now is just type /release_pets and it will auto kill all pets
so far been working for me when the bug does crop up

took my MM to rogue, Couldnt get the pets to do anything when i finally goto to Blueside. Logged for the night next to Manti. Came back the next day on a full system restart summoned pets..... ...zoned at the Bricks/Ip door....attacked some stuff....upgraded and attacked more stuff.....everything was fine. Zone back through bricks....still following me. Used the tram and same behavior as yesterday, they wont do squat in the zone.