Maybe double check to see if you have it set to RGB instead of RGBA under the output tab? I believe it’s set to RGB by default in versions 2.79 and earlier, which is not ideal.
If you’re in 2.8 or later, try doing View > Viewport Render Image with Viewport Shading on and see if the problem persists. While you’re at it, try and make sure you’re not accidentally rendering the World Background or the Viewport Background.
Going off of the first point, which applies to both main version types, make sure when you hit Save As on the final render that you also have it set to RGBA instead of RGB in the file saving menu!
I’m not well-versed in GFX or rendering, but I hope this helps a little nonetheless. Good luck!