I may be pointing out the obvious, but...

Professor Quirrell closed his eyes. His head leaned back into the pillow. "You were lucky," the Defense Professor said in a soft voice, "that a unicorn in Transfigured form... did not set off the Hogwarts wards, as a strange creature... I shall have to... take this outside the grounds, to make use of it... but that can be managed. I shall tell them that I wish to look upon the lake... I will ask you to sustain the Transfiguration before you go, and it should last long enough, after that... and with my last strength, dispel whatever death-alarms were placed to watch over the herd... which, the unicorn being not yet dead, but only Transfigured, will not yet have triggered... you were very lucky, Mr. Potter."

This is how the troll was smuggled into Hogwarts without the wards going off. In all likelihood, Quirrell had the transfigured troll on his person when Dumbledore identified to the Hogwarts wards "The Defense Professor stands within this circle". Trolls self-transfigure as a form of regeneration, so the transfiguration would not kill the troll or be detectable.