We report on the experimental observation of "focus splitting" when light is tightly focused into a uniaxial lithium niobate crystal along its optical axis. This effect consists in the focal spot being split into two major sub-peaks along the axial direction. For the microfabrication applications such as three-dimensional photonic crystal fabrication and waveguide writing, this effect is highly undesired since it can lead to the generation of multiple distinct voxels in the vicinity of the focus. The splitting is caused by different birefringence induced aberrations for the ordinary and extraordinary polarization eigenmodes. We present numerical simulations which support our observations and suggest methods to avoid this effect.