The variables 'PixelCornerLatitudes' and 'PixelCornerLongitudes' contain the coordinates of the corners of each pixel. The corner locations fall on either side of the pixel centers, which are defined in the geolocation variables 'Longitude' and 'Latitude' having the dimensions nTimes and nXtrack. Extra elements are needed to define all four corners for each pixel, so the dimension sizes of the corner variables are (nTimes+1) and (nXtrack+1). Variables in the subset output files are cropped according to the mask, which is based on the nTimes and nXtrack dimension sizes. Because the dimension sizes of the PixelCorner variables do not match all the other variables in the file, they do not get cropped.
Note that this issue does not apply to all data products from OMI.
If you require cropped pixel corners, there is another product, OMPIXCOR (https://disc.gsfc.nasa.gov/datasets?key ... COR&page=1
), that contains pixel corner information that will crop as you expect. Enter the same search criteria for OMPIXCOR that you entered for OMHCHO, and the cropped data for the two will correspond to one another.