Debugging quantum states transformations is an important task of modern quantum computing. The use of quantum tomography for these purposes significantly expands the range of possibilities. However, the presence of preparation and measurement errors complicates the practical use of this procedure. In this work, we investigate the possibility of estimating these errors from experiment. These estimates are subsequently used to build a robust quantum tomography model. The model allows one to accurately reconstruct unitary errors of singlequbit gates. We show that, having such imperfect single-qubit gates with pre-estimated errors, one can obtain transformations close to ideal ones. A similar approach can also significantly mitigate single-qubit gates crosstalk.