The Train IsoCluster Classifier tool works on the entire input image. The warning message is given to prevent the tool from accidentally being run on a global image service.
The input raster is too big. Either the width and height are both greater than 50,000 pixels, or either the width or height is greater than 200,000 pixels.
Set the Extent environment to less than 50,000 by 50,000 pixels, or less than 200,000 pixels in either the x or y direction. Extent needs to be defined in map coordinates.