muons are produced following the decay of other cosmic rays known as mesons. Increasing the temperature of the atmosphere expands the atmosphere so that fewer mesons are destroyed on impact with air, leaving more to decay naturally to muons. Consequently, if temperature increases so does the number of muons detected.
Ref.: Sudden stratospheric warmings seen in MINOS deep underground muon data. S.M. Osprey et al., Geophys. Res. Lett. in press.