I’ve been trying to clip a particular webpage (m.seriouseats.com/2013/03/the-fo … -home.html) and no matter how I do it, the only image that’s included is the 1st. Otherwise, there are just place holders for the images. I’ve checked all of the settings, and can’t find anything that should be causing this, that I’m aware of.
In the meantime, you can always use Safari Reader Mode then Print, in the PDF menu in the bottom left there is Save PDF to DEVONthink Pro, that kept the images for me at least.