The Halifax had several problems in its earlier forms, the nacelles and many of the exhaust styles for the Merlin installation were very draggy (the aircraft as a whole was a bit draggy too). Added to this were prop vibration, poor exhaust flame damping and those famously dangerous triangular fins. This doesn’t cover all the problems, but gives some idea. It’s enlightening to note that loss rates on Merlin Halifax squadrons were worse than those of the Stirling, and it’s only the record of the later Halifax models that saves the type from being remembered as the worst of the RAF heavy bombers.
There were refinements as production went along, so by the time the switch had been made to Hercules power with the Mk.III, the airframe was in a much better state to make use of the extra power and the aircraft was aerodynamically safe to fly.
Very late in the war the Hercules 100, with a redesigned intake and surpercharger, became available and these were fitted to Mk.VI Halifax. Combined with the extended wing tips, this made for a leap in ceiling and overall performance.