Schliemann was not a professional archaeologist and some scholars critiqued his excavation skills, saying he destroyed important archaeological evidence and mixed up artefacts from different time periods and layers of Troy.
He was a Homer fan who desperately wanted to find the Lost City of Troy - he, therefore, treated Homer as a historian rather than a poet, and used the Iliad as a guidebook rather than fiction. This meant he may have taken some of the descriptions and artefacts in the poem a bit too literally.
Since Troy existed thousands of years ago, it is difficult to pinpoint the location based on a description that was written hundreds of years after the time it is describing. There is too much room for inaccuracy.