Just to clarify a few things:
The distance an object moves per frame is speed*dt, so with a speed of 5000 the object will move 5000/60 or about 83 pixels per frame, which is why it can pass other objects without colliding.
For doing an instant hit, the common approach is called "ray casting", but you can also find examples on the forum about lasers that do it too. By using a sprite and changing the width you can do the same thing as the line segment idea.
That error is a bug I'd say, and a good candidate for an error report.
Your last issue is probably something simple, but we'd need to see a capx to find it. The posted events don't seem to cause it.