Transparency is the artistic effect that lets the viewer see through an object in an image. It’s also used to create shadow and glow effects.
To avoid problems, don’t use transparency over a spot color. Converting the spot color to CMYK and flattening the image will prevent issues when the image is printed.
The image below shows one type of transparency issue that can show up in printing. In this case, a white box appears when it's not supposed to.
Image source: InDesign Secrets