Murphy said it had been “massively difficult” to balance his squad on two fronts as a number of injuries and suspensions took hold on his group.
In recent weeks, Ulster have lost key players such as Stuart McCloskey, Jacob Stockdale, Angus Bell, James Hume and Rob Herring through injury.
Ulster have also missed captain Iain Henderson, who will also sit out next week’s final, and Harry Sheridan through suspension at the tail end of the season.
“It’s the fact that you don’t get a break,” Murphy added.
“It’s 10 weeks into a block now where we’ve played every week and there’s no time for refreshment.”
Murphy pointed to how Glasgow and the Stormers have benefited from having off weeks due to their respective European exits and that allowed them to keep their squad fresh.
He said that, due to the run of games, Ulster usually have “one training session and a captain’s run” in the lead-up to games.
“We have a fair few bodies who are not technically injured, but they’re also carrying a lot of mileage in their legs.
“Our team selections have to balance up the what we need from a freshness point of view and what we need from a competitive point of view as well, or a game time point of view.
“It’s a massive balancing act, but tonight we’re bitterly disappointed to come away with a loss.”