i assume you're using switchcamera to see through the sniper scope, in which case the waypoint indicator will show for that character if it has waypoints, or belongs to a group which has waypoints - as flaber says, playing in vet mode is a quick fix for this, but not complete. if this is for a cutscene, use empty markers and the
unit_name domove getmarkerpos "marker_name"
command to move the sniper instead of waypoints. presto, no more waypoint indicators.