There is an option at the top right of your Meme Branding Tool called "Manage Layers." You can go there and delete each layer that has multiple "copy" next to it (select the circled X to the right of the layer). In the image below, I show an example. This is a double copy of the text box.
If you made multiple copies of a text box, you'll want to be sure you do not delete your text boxes. You can do this by keeping an eye on your meme branding bar and ensuring that only the logos are disappearing.