There might have been multiple separated inbreeding groups. Yes these groups are related among themselves but not inter-group.
Perhaps you're off by a 0 or two...?
The Americas may have been clearly separated for a while, but they have done so much interbreeding with people from other continents since 1492, that the common ancestor is more recent than that.
"Monte Carlo simulations suggest the MRCA was born surprisingly recently, perhaps even within the last 5,000 years, even for people born on different continents."