It's just a function of how the game mechanic works. The same thing happens if two ships are sitting in side by side sectors within a system. Doesn't have to be at a warp point. If each gets orders to move to the other guys sector and the ships have the same speed, they will pass like ships in the night.
If one ship is faster then the other though, combat will occur.
[ April 23, 2004, 14:35: Message edited by: geoschmo ]