Sorry for the trouble. This behavior is indeed due to later updates to macOS; we originally came across this in our testing of High Sierra, and this issue was addressed in the latest versions of OmniGraffle 7 for Mac. https://support.omnigroup.com/high-sierra/
It looks like you’re currently running OmniGraffle 6, which is no longer in active development, and was last updated in 2016 for macOS Sierra 10.12. As a result, the app does not contain any compatibility fixes for High Sierra or Mojave. Depending on the stencil, you may experience better results in OmniGraffle 6 on Mojave by switching to one of the other Stencil inspector view modes, using the icons to the right of the Filter search bar.
We don’t have any future updates for OmniGraffle 6 planned at this time. OmniGraffle 7 was released on October 10th, 2016, and has since been fully updated for compatibility with Mojave. We’re happy to offer an upgrade discount for existing customers; information about how to upgrade at a discount is available on our site here.
You can learn more about OmniGraffle 7 and download a free 14-day trial of the app from our OmniGraffle website. Hope this helps!