Why is this happening?
Last I recall (from many years ago, but I don't think Steve has changed it), Steve looks at the course of each missile salvo and/or ship and tries to find other ships whose detection range it will enter during its move. If it finds one, it tries to predict how much to shorten the impulse so that the mover just barely enters detection range.
My recollection is that this didn't always work. I work around this by saving the game when I think a hostile encounter is possible (e.g. when probing a new system). If I land ridiculously close to something that I should have detected, then I roll back to the save and do the same thing with shorter time steps (starting out long to get in the neighborhood, then shortening as appropriate).
John