Large energy released in PionPlusInelastic and PionMinusInelastic process was observed during single pi+ and pi- simulation in the whole ATLAS environment (Athena 12.0.3). For example, among 500 events of 50GeV single pi-, 5 hits were found with too large total energy of secondary pions - energy released in nuclei interaction was >1000MeV. See output /afs/cern.ch/user/p/pospelov/public/large_invisible.txt obtained with code http://alxr.usatlas.bnl.gov/lxr/source/atlas/Calorimeter/CaloG4Sim/src/SimulationEnergies.cc
Which physics list and version of Geant4 did you use? It will help to know if it was LHEP or QGSP, so I can find out which model was invoked.
Re-assigning to Gunter Folger, our QGS expert.