If time-reversal symmetry is broken at the surface of a topological insulator, a gap could open at the Dirac point of the topological surface state. The Dirac point, where forward- and backward-moving electrons have the same energy, is located at a time-reversal invariant momentum point (also called a Kramer's point) in the reciprocal space (the crystal momentum is zero or zero plus an integer multiple of a reciprocal lattice vector). The Kramer's pair of surface state branches defined for forward- and backward-moving electrons, which would otherwise be degenerate at k = 0, are no longer degenerate as a result of a time-reversal symmetry breaking interaction which couples differently to different spins.
For a superconductor, the energy gap forms at the Fermi energy (binding energy = 0). The condensate of Cooper pairs has a lower energy than the Fermi energy of the normal metal state, while unpaired electron states exist above the Fermi energy. Hence, a gap forms. The hope is that Cooper pairs will tunnel from a superconductor onto the surface of a topological insulator in proximity to it, creating a similar gap in the topological surface state.
So, these are two distinct kinds of gaps in different regions of the band structure which signify very different kinds of order.