Hello,
1) Coud you, please, provide me screenshot of product categories with the png images and bg color that you want to remove. Because product categories on the front page are jpg images with bg http://prntscr.com/s86iz5
2) Add the following code to Theme Options > Custom CSS to remove the black bg color for the popup
.pswp__img--placeholder--blank {
background: transparent;
}
Regards