Erm...no...there is no such rule, at least not till this year... we were simply drawn like that in the last years, last time, if the hour isn't killing my memory, was when we played Bayern and Chelsea in the QF/SF at home in the 1st leg simply because Barca was taken out first out of the pot.
They had an intention, yes, some 3-4 years ago to create "an year" coefficient counting points in the Group Stage + Round 2 ( R16 ) to make two different pots in the Quarter Finals so there won't be a mess up like Barcelona-Real in one draw and PSV-Fener in another... the idea fell because CL always had no restrictions starting in the QF, making anything possible from then on.
Also, the differences between 2 teams could be 0 many times, if for example one team had 11p in the group stage, 1 vic and 1 draw in the R16 and another 13p in the GS and two draws in R16.