In the past there have been situations where a team has designed a car or part. At this point the design is legal. They race and they absolutely batter the opposition. The FIA intervene and ask them to re-design their vehicle to remove the part that is giving them such a huge advantage. Even at this point, the FIA do not render that design illegal, however, in the interests of sportsmanship, ask the team to make the changes.
The above has happened numerous times in the past when a particular design has given a single team, too big an advantage.
Obviously it depends just how much of an advantage the team is gaining. If its 0.5s/lap, the FIA is unlikey to interfere. If however, it gives a team 2s/lap advantage, the FIA will intervene.