Who was in Rebecca's womb? She was carrying two individuals, yes. But, God foresaw two nations, two peoples, and He clearly informs Rebecca of that truth. It is from this vantage point that God foretells her that the "the older shall serve the younger". In other words, the nation that descended from the older brother would serve the nation that descended from the younger brother. This passage offers no prophesy regarding the two brothers as individuals.
In their lifetimes, Jacob came far closer to serving Esau, than Esau ever came to serving Jacob. Therefore, if this prophecy referred to the individuals, it failed! Since God’s prophecies cannot fail, this prophecy of the younger’s supremacy must not be referring to individuals.
And in case you think this is the only place God refers to Esau and Jacob as nations:
The burden of the word of the LORD to Israel by Malachi. "I have loved you," says the LORD. "Yet you say, 'In what way have You loved us?' Was not Esau Jacob's brother?" Says the LORD. "Yet Jacob I have loved; But Esau I have hated, And laid waste his mountains and his heritage For the jackals of the wilderness." Even though Edom has said, "We have been impoverished, But we will return and build the desolate places," Thus says the LORD of hosts: "They may build, but I will throw down; They shall be called the Territory of Wickedness, And the people against whom the LORD will have indignation forever. (Malachi 1:1-4)
The Edomites, descendents of Esau, were a "people against whom" God’s wrath and indignation moved. They were "hated", because they were wicked. However, this "hatred" is not absolute, but relative. The word, "hatred", is only raised in contrast with God’s "love" for the people of Jacob. (Please, recall that the Edomites were blessed with land and nation as well. Also, compare to Jesus’ usage of "hatred" toward family relative to the required "love" for Him, Luke 14:26.) In this quoted context of Malachi 1, the ultimate distinction between Esau and Jacob was that God spared a remnant from Jacob's seed, through whom came the Messiah, but Esau's seed were destroyed. This context shows applicability to the role of the nations, not the salvation of the original fathers.