I ran into two hot lines when replacing a three way switch
It's possible that you are detecting residual voltage from the neutral through the lamps at one switch (in the order of 50V often), you can use a multimeter in voltage mode and see how much voltage you actually detect. Or take out the bulbs from the fixtures and check again.

Other wise you can (with the breaker off) connect 2 wires at one switch then check continuity of the wires at the other end (with a battery and little bulb for the poor-man's checker). If the non-lives are those that connect on both ends then it's fine.