I'm also experiencing this... came out of the blue. I clip dozens of articles each week into my Evernote database from all across the internet (PDFs as well as full webpages and images). I used to get this error once every month or so. Now probably about 80% of the pages I try to clip need to be reloaded. Sometimes it takes 3-5 refreshes for the web clipper to work. I'm experiencing this on Chrome across both Windows and macOS Sierra.
Same issue - on OS X Yosemite/Chrome 45. Clips multiple tabs, sources the wrong text, creates blank notes. All sorts of problems - it's basically unusable and has brought my research to a screeching halt