A major turning point arrived at the start of extra-time when Murphy and Jason McGee were among four players shown black cards following a melee at the end of normal time.
McGuinness felt the sanctions made an already difficult task even harder.
“It didn’t help matters, and we didn’t know what was going to happen heading into the dressing room,” he said.
“When you have two men down, it’s hard enough under the new rules. Teams are looking for those spaces, and that’s what happened.
“The lads were trying their best, but Dublin had fresh players coming in off the bench while some of our lads had played the whole game.”
The Donegal manager also pointed to the increased physical demands of the new rules, arguing that the intensity of games has risen significantly.
“The games are probably 30 or 35 per cent more intense than before,” he added.
“You’re trying to manage players and get as many healthy bodies to the line as possible. Every county is dealing with that.”
Having entered the championship as one of the favourites after reaching last year’s All-Ireland final, McGuinness believes Donegal ultimately paid the price for inconsistency.
“There are a lot of talented players in that dressing room, and they’ve shown that over the last number of years,” he said.
“But it’s consistency. That’s what it’s about. We just weren’t consistent enough.”
Donegal’s season is now over, while Dublin march on to Monday’s quarter-final draw.
