In the methods of compensating for an alignment error during fabrication of structures on semiconductor substrates, a conductive pattern structure is formed at a first position on a first semiconductor substrate. The conductive pattern structure includes a grid of first and second conductive patterns arranged as columns and intersecting rows with openings bounded therebetween. A first conductive contact structure overlaps the conductive pattern structure, and includes a plurality of spaced apart conductive contacts arranged as a grid of rows and columns that can be tilted at a non-zero angle relative to the grid of the conductive pattern structure. A determination is made as to whether the first conductive contact structure is electrically connected to the conductive pattern structure. A second conductive contact structure is formed at a position on a second semiconductor substrate that is determined in response to the determination of whether the first conductive contact structure is electrically connected to the conductive pattern structure.