Preparation of an Al-Ni alloy for transmission electron microscopy (TEM) by focused ion beam (FIB) milling using Ga⁺ ions induced phase transformations, risking misinterpretation: from FCC Al-Ni solid solution to FCC Al-Ni and orthorhombic Al₃Ni phases. Upon milling a nanolaminated Al₉₅Ni₅ - AlO_x thin film with Ga⁺ ions, local Ga segregations of up to 15 at.% and the concurrent formation of orthorhombic regions are observed. This is consistent with density functional theory calculations indicating that the orthorhombic structures with and without Ga are more stable than the corresponding FCC compositions probed here. In contrast, Xe⁺ plasma FIB preparation did not alter the microstructure and the maximum Xe-content reached only 0.2 at.%. TEM-analysis did not reveal significant strain differences of the Al-Ni solid solution and Al₃Ni. Hence, we recommend the use of Xe⁺-pFIB for sample preparation of alloys which are sensitive to Ga-induced phase transformations such as Al₉₅Ni₅ to prevent misinterpretation.