flight rust ? at the Mitsubishi Outlander

Have an outlander bj.11.2007 with 140ps vw-motor and had to find out now unfortunately that he, below the side windows to the floor, is covered with rust points. sorgar under the plastic of the rear number plate (mount removed) which can be found, in total it probably 2000 points, I am sure that in the autumn were not there yet, the workshop told me today that this would not be a guarantee case, because it should come to it by any environmental influences, who has already a n similar problem had or tips for me, oh yes the complete car polishing costs 1000 euro.