The Disconnect extension (v3.0.3) for Safari seems to interfere with the Clip to Devonthink (v1.2.6) extension. Clicking the nautilus icon in Safari opens the dialog but clicking the clip button in the dialog produces a bookmark instead of a PDF+Text in Devonthink Pro Office (v2.8.6).
I cannot speak to the effect of the extension or not, but reboot your machine. If our extension runs into an issue, it will use Bookmarks as a fallback.