You'd think someone would catch the creepy factor when they were viewing the dailies.
By the time dailies arrive it's probably too late. Television production doesn't always have the time and money to have the line rewritten, haul back all the actors, and reshoot the scene. If they cut the line out completely, then the show comes up short on running time and they have to make up for it some other way. These sort of things should have been caught by the director during shooting when there might have been time to fix it. Any line changes always had to be approved by the producers, improvised lines were rarely allowed.
With the Adult Wesley business, the scene probably wouldn't have raised any eyebrows at all if Troi or Yar had delivered the "Not bad" line.