In rocker assembly design there is what is called overlap, this is a short period when both intake and exhaust valves are open at the same time to scavenge the cylinder.
During this process, the incoming charge will push- out any remaining burnt gases in the cylinder, if this process persist, the incoming charge will escape with the burnt gases.
The back pressure in the exhaust line normally will create some resistance to flow, in the absence of this resistance to flow due to a busted muffler or exhaust line will certainly result in loss of incoming charges.