Lasers, like all light, are only visible if they bounce off something and the light arrives at your eyes. Air is famously mostly transparent so a laser going through air isn’t going to leave much of a visible path. The point where it actually hits the object it is directed at will be much brighter so that is where the missile or bomb will aim for.
The laser itself will often have a shroud around it to reduce the visibility of the origin. Not mainly because the guided munition might confuse it for the target, but because an enemy could determine where you are by looking at a bright laser emitter. Lasers are also famously very directional so again the spot where it is pointed will be much brighter than the emitter unless it is pointed directly at the viewer. Unless the person using the designator is pointing it directly at the guided munition it shouldn’t be subject to confusion.
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