In the present work, we studied the magnetization, vorticity, Cooper pairs density, and the spatial distribution of the local magnetic field in a three-dimensional superconductor with a SQUID geometry (a square with a central hole connected to the outside vacuum through a very thin slit). Our investigation was carried out in both the Meissner-Ochsenfeld and the Abrikosov state solving the two-band Ginzburg-Landau equations considering a Josephson coupling between the bands. We found a non-monotonic vortex behavior and the respective generation of vortex clusters due to the Josephson coupling used between condensates.