Schliemann dug straight through the actual Troy that he was looking for, destroying a huge chunk of it to get to an even earlier settlement in the strata beneath that he decided to call Troy. His "method" was essentially do dig a trench all the way to the bottom, assuming that the oldest level would be Troy. (Yes...he was that stupid).

It was only afterwards that other, actual archaeologists placed the proper stratum that the homeric Troy would have existed in. And by then, much of it was already obliterated.

I majored in Near Eastern Classical Archaeology with a focus on the Bronze age (Hittites, Minoans, Mycenaeans, Babylonians, etc...), and lesson one may as as well have been titled "Why Heinrich Schliemenn was an asshole."