OpenCV draw rectangles around only large contours?

first time posting, hope I put the code in the right way.

I'm trying to detect and count vehicles in a video, and so if you look at my code below I find the contours of the image after thresholding and dilating, and then I use drawContours and rectangle to draw a box around the detected contours.

I tried to put a filter on the drawContours/rectangle if statement by saying if the area of the rectangle isn't bigger than 40,000, then don't draw it.

Now if you look at the picture I attached, you'll see that there are rectangles that are drawn inside the larger rectangles, which I am not trying to do. enter image description here. These rectangles has an area less than 40,000 but they are being drawn for some reason.

I was going to use the rectangles to count the cars on the image, but if that's not the best way to do it I'm open to suggestions.

Thanks.

using namespace cv;
using namespace std;

int main()
{
    VideoCapture TestVideo;                 //Declare video capture
    Mat frame;                              //declare Mat as frame to grab

    TestVideo.open("FroggerHighway.mp4");           //open the test video from the project directory

    if (!TestVideo.isOpened())              //If its not open declare the error
        {
            cout << "Video did not open." << endl;
            waitKey(0);
        }

    if (TestVideo.get(CV_CAP_PROP_FRAME_COUNT) < 1)     //If the frame count is less than 1, basically an error checker
        {
            cout << "Video file must have at least one frame." << endl;
            waitKey(0);
        }

    TestVideo.read(frame);                              //read the first frame
    Mat frameGray = Mat::zeros(frame.size(), CV_8UC1);  //Convert frame source to gray
    cvtColor(frame, frameGray, CV_BGR2GRAY); 

    Mat frame2 = Mat::zeros(frameGray.size(), frameGray.type());    //Intermediate frame
    Mat framediff;                                                  //Frame differencing
    Mat thresh;
    Mat element;                                                    //Element used for morphOps (dilation)
    Mat dil;    

    while (TestVideo.isOpened() & waitKey(30) != 27)                //while the video is open, show the frame, press escape to end video
        {
        absdiff(frameGray, frame2, framediff);                      //take absolute difference of both frames
        threshold(framediff, thresh, 22, 255, CV_THRESH_BINARY);    //If absdiff is greater than 22, turn it white. 

        namedWindow("Gray", CV_WINDOW_NORMAL);                      //Display gray video
        imshow("Gray", frameGray);

        namedWindow("FrameDiff", CV_WINDOW_NORMAL);                 //Show frame difference before threshold/dilation
        imshow("FrameDiff", framediff);

        namedWindow("Threshold", CV_WINDOW_NORMAL);                 //Show thresholded video
        imshow("Threshold", thresh);

        element = getStructuringElement(MORPH_CROSS,                //morphOps dilation
            Size(2 * 5 + 1, 2 * 5 + 1),
            Point(5, 5));
        dilate(thresh, dil, element, Point(-1, -1), 1, 1, 1);

        namedWindow("Dilation", CV_WINDOW_NORMAL);                  //Show dilated video. 
        imshow("Dilation", dil);

        //Apply findCountours function to draw countours and count the objects.
        vector<vector<Point> > contours;        //Not sure what this does but it works
        findContours(dil, contours, RETR_EXTERNAL, CHAIN_APPROX_SIMPLE);    //(outout image, hierarchy, and 2 ways to calculate it)
        vector<vector<Point> > contours_poly(contours.size());      //Also not sure what this does
        vector<Rect> boundRect(contours.size());            //This is used to approximate a polygon to fit the contours it calculated I think

        Mat output = Mat::zeros(dil.rows, dil.cols, CV_8UC3);   
        int counter = 0;                                    //Used to count # of rectangle drawn

        for (int i = 0; i < contours.size(); i++)
        {
            approxPolyDP(Mat(contours[i]), contours_poly[i], 3, true);  //Approximates a polygon to fit the contours calculated ?
            boundRect[i] = boundingRect(Mat(contours_poly[i]));    //for each approximation, a bounding rectangle is sorted around the contour ?

            if ((boundRect[i].x * boundRect[i].y) > 40000)          //If the bounding rectangle has an area less than 40,000 then just ignore it completely
            {
                counter = counter + 1;
                drawContours(output, contours, i, Scalar(255, 255, 255), -3);   //(input, countors, contour to be drawn, color of it, thickness (negative fills image));
                rectangle(output, boundRect[i].tl(), boundRect[i].br(), Scalar(0, 0, 255), 2, 8, 0); //Draws the actual rectangle around the contours
            }
        }

        cout << "Rectangles Drawn: " << counter << endl;

        namedWindow("Output", CV_WINDOW_NORMAL);
        imshow("Output", output);

            if (((TestVideo.get(CV_CAP_PROP_POS_FRAMES) + 1) < TestVideo.get(CV_CAP_PROP_FRAME_COUNT)) & (waitKey(30) != 27))   //Move the frame count up 1, show the frame
            {
                TestVideo.read(frame);
                frameGray.copyTo(frame2);                   //MUST USE copyTo, or clone! Can't do frame2 = frameGray*
                cvtColor(frame, frameGray, CV_BGR2GRAY);
            }
            else
            {
                cout << "End of Video" << endl;
                waitKey(0);
                break;
            }

            waitKey(30);        //wait 30ms between showing each frame
        }

    return (0);
}

You're multiplying the x and y coordinates to get the area of rectangle, you should be multiplying the width and height.

//If the bounding rectangle has an area less than 40,000 then just ignore it completely
if ((boundRect[i].width * boundRect[i].height) > 40000)          
{
// code here
}