Is it frequent to use two Ethernet cables for one phone line?
Probably you have two or more phone jacks daisy-chained together.  One cable goes to wherever the phone line enters the house and the other runs to another phone jack somewhere else in the house.

This is a common practice. I did some pricing online, and it seems that Cat 5e is comparable in price to 4-conductor phone cable, so the builders may simply have used it because they had it to hand.