It is now well established that in two-dimensional chiral p-wave paired superfluids, the vortices carry zero-energy modes which obey non-abelian exchange statistics and can potentially be used for topological quantum computation. In such superfluids there may also exist other excitations below the bulk gap inside the cores of vortices. We study the properties of these subgap states, and argue that their presence affects the topological protection of the zero modes. In conventional superconductors where the chemical potential is of the order of the Fermi energy of a non-interacting Fermi gas, there is a large number of subgap states and the mini-gap towards the lowest of these states is a small fraction of the Fermi energy. It is therefore difficult to cool the system to below the mini-gap and at experimentally available temperatures, transitions between the subgap states, including the zero modes, will occur and can alter the quantum states of the zero-modes. We show that compound qubits involving the zero-modes and the parity of the occupation number of the subgap states on each vortex are still well defined. However, practical schemes taking into account all subgap states would nonetheless be difficult to achieve. We propose to avoid this difficulty by working in the regime of small chemical potential mu, near the transition to a strongly paired phase, where the number of subgap states is reduced. We develop the theory to describe this regime of strong pairing interactions and we show how the subgap states are ultimately absorbed into the bulk gap. Since the bulk gap vanishes as mu -> 0 there is an optimum value mu_c which maximises the combined gap. We propose cold atomic gases as candidate systems where the regime of strong interactions can be explored, and explicitly evaluate mu_c in a Feshbach resonant K-40 gas.
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