I fear I can't help you much on the matter since I can't see it visually. I remember one mission in particular in which I was wandering around aimlessly, killing waves after waves of Alien trying to figure out what to do... If I remember well there was one last object hidden somewhere on a kind of "cliff" that I did not noticed until then.
Anyways, if you really can't find out just save your game and try to exit the building to see if you succeeded in destroying the building. If everything fail try the mission a second time after realoading/healing your troops, the map will most probably be different and you might just win it the second time without problems.
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