Basically, because men and women don't always travel together. If we look at more modern population mix, Puerto Rico has about 60% of the population with Native American mt-haplogroup, 25% African and 15% European. On the Y side, 85% European and 15% African.
What do you think happened there? And what make you think the same didn't happen in ancient times as well?
The formation of Puerto Rican Y DNA/mtDNA is not similar to the formation of *Pre-Historic* European Y DNA/mtDNA but is sort of similar to the formation of *Modern* European Y DNA/mtDNA. Puerto Rico(men travelling more than women) can not give an answer as to why European Y DNA/mtDNA throughout history was/is the way it was/is.
Puerto Rican mtDNA/Y DNA is somewhat similar to Modern European mtDNA/Y DNA because there's sex bias admixture. Admixture between Steppe and West Asian Chalcoluthic/Bronze age newcomers and native Neolithic/Mesolithic(EEF, WHG)-descended Europeans in Europe was probably(not for sure) sex bias. However, a big difference is in Puerto Rico there's a diverse array of Spanish Y DNA while modern Europeans belong to a select handful of literally 1,000,000s of Steppe(and West Asian J2b and E-V13?) Y DNA lineages. As far as I know there were no mega-Y DNA Spanish fathers in Puerto Rico as there were mega-Y DNA Steppe(and two WHG/EEF fathers; I1 and I2a1b. And West Asian?; J2b, E-V13, etc.) fathers in Europe, instead there are probably 1,000,000s of different Spanish Y DNA lineages.
The phenomenon of what I call mega-fathers is why mtDNA and Y DNA have different diversity in essentially every human population. There are also mega-mothers but they're usually less frequent.
All four of the Mesolithic/Neolithic ancestors of Europeans belonged mostly to mega-father Y DNA haplogroups, this was long before the expansion of R1b-L151 and R1a-M417, it has nothing to do with them. Most WHGs(ruled most of Europe) belonged to I2a1, most Neolithic Anatolians belonged to G2a2, most Mesolithic Caucasins belonged to J, most Mesolithic Russians belonged to R1a1 and R1b1. Each group had more mtDNA diversity than Y DNA diversity. The West Asian ancestors; Anatolians and Caucasins, especially had more mtDNA diversity than Y DNA diversity, and are the source of essentially all European mtDNA that isn't U5 or U4 or U2.
We see the same pattern with Y DNA O in NorthEast Asia(China, Japan,and Korea), Q1a in Native Americans, N1c in Finno Urgics, J1 in Arabs, E1b in Africans, the list goes on and on and on. The expansion of R1b-L151, R1a-M417, I1, I2a1b, E-V13, N1c, in Europe may be more extreme and more recent(expanded within a couple thousend years), but might be caused by similar things as mega-father Y DNA haplogroups around the world.