I can not reproduce that, but it might depend on the image, so if you can attach the Gimp 3 .xcf file.
Things to try, you can add an effect without it becoming an (fx) layer. There is a merge check box in the dialogue. Otherwise merge the filter from the layers dock.
Things to try, you can add an effect without it becoming an (fx) layer. There is a merge check box in the dialogue. Otherwise merge the filter from the layers dock.