The magnetic-flux quantum (Φ0) cannot be generally divided into smaller ones in a usual superconductor. If a subdividing path is present, the science and technology of the superconductor drastically change. In previous studies, we experimentally presented a new, easy way to subdivide Φ0 into smaller quanta (Φf) using an ultrathin Nb bilayer with a through-pinhole (H. Ishizu, H. Yamamori, S. Arisawa, K. Tokiwa, Y. Tanaka, Physica C 595 (2022) 1354029.). However, because of an experimental technical problem, we could not use a higher field to generate more than one Φf. It was not clear if multiples of Φf could be trapped in a pinhole (in a usual superconductor, multiples of Φ0 are trapped in a pinhole). In this study, we observed multiple fractional phase shifts with a direct-current superconducting interference device (SQUID) placed on an ultrathin Nb bilayer disk containing a through-pinhole using an improved modification of an experimental procedure. The phase shift for the SQUID with the bilayer disk is an integer multiple of a basic fractional phase shift divided by 2π. However, we did not observe the fractional phase shift for a SQUID with a single-layer disk. These observations indicate that multiple fractional flux quanta are trapped in the bilayer disk. According to the vortex-molecule model, if the vortex molecule is larger than the bilayer disk, such quanta can be trapped. This is one example of altering a fundamental (universal) physical constant. The SQUID can more sensitively detect Φf than Φ0, rendering the design of novel superconducting electronics possible.