I would have to see said pixels to tell you for sure, and know whether you're trying to save to .gif format - if you are, just save your frames as .PNGs and import into GIMP, Photoshop's indexing/GIF features are annoying.
Assuming you're saving to .png:
If they're not along an edge, just use the eraser tool at max opacity on the final .PNG image. Alternately, if they're over something opaque, zoom in on each spot and blink the visibility of each layer until you find the layer they're on.
Incidentally, there's no reason under the ever-loving sun to use that GIMP function except to save file space. It only works on 0% opaque pixels, so your semi-transparent ones won't even get touched!
Photoshop treats the alpha channel differently. In GIMP, erasing effects only the alpha (transparency) channel, while in Photoshop... let's just say transparency-lock a layer and using the smear tool in the 0% opacity -> 1%+ opacity direction does something pretty dang interesting.