If your image editor supports importing color palettes, you should use SLADE to export the SRB2 palette, then import it into your image editor. From there, you can most likely change the image format into a paletted one and select the SRB2 palette to use. Paletted images don't support transparency, so you'll be able to see any erroneous areas easily in the image editor.
Since you already have an image here, you should export it using SLADE and then import it into your image editor. It should be pretty easy to remove the black spot from there. Then just save it and import it back into the addon file.