For some reason one of my sprites has duplicated itself and I can's get rid of it, it doesn't register as a sprite in the sprite box and it isn't part of the background. How do I get rid of it without deleting everything?
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That's a pretty common glitch. Go up to the tools above the stage and select the one that looks like a pair of scissors. Then click the glitched sprite, and it'll disappear.
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Cloud it have stamped its self? If so, go to "pen" and run the "clear" block.
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