When they say 3 megapixels, that's exactly what they mean. File size isn't the issue; resolution is. How big are the images they're rejecting (pixel width x height)?
If you're shooting small objects, either you're going to need to use a macro lens (or the macro mode on a fixed lens camera) to make them fill the frame or at least fill enough of it to exceed the minimum pixel count after cropping; or you're going to have to put several of those objects in the picture.