Yes, I got the same trouble several times. I think raising mountains is considered an hostile act as you will dry out your neighbor's land, but I'm not sure.
I even got something stranger, I was playing Sven and had a Pact with Roze, together, we wiped out Marr, and then I decided to sink my conquered bases as I was better in the ocean, but despite all the lands that would have been flooded by the operation were in my territory, I was not allowed to do this without canceling my Pact first

, obviously, AC does not manage territory very well.
But, I finally managed to do what I wanted without breaking my pact, I made a few very industrial bases, star polluting, and then let the sea rise

(ah, I was planetary gov, so I vetoed the solar shade

)