We present a theoretical study of a system consisting of a superconducting island and two quantum dots, a possible platform for building qubits and Cooper pair splitters, in the regime where each dot hosts a single electron and, hence, carries a magnetic moment. We focus on the case where the dots are coupled to overlapping superconductor states and we study whether the spins are ferromagnetically or antiferromagnetically aligned. We show that if the total number of particles is even the spins align antiferromagnetically in the flatband limit, i.e., when the bandwidth of the superconductor is negligibly small, but they align ferromagnetically if the bandwidth is finite and above some value. If the total number of particles is odd, the alignment is ferromagnetic independently from the bandwidth. This implies that the results of the flatband limit are applicable only within a restricted parameter regime for realistic superconducting qubit systems and that some care is required in applying simplified models to devices such as Cooper pair splitters.