I fixed it already by accident. Turns out it was because I had stacked a png background over a normal JPG background. Once I switched t an only JPG Background, the clones all disappeared. Thanks for helping though!
I had a feeling it was a problem with transparency, which JPG images do not have. Also, you probably had the PNG image (or at least one of them) saved in a static field, which allowed it to carry over into new worlds (when resetting).