Sorry about the inconvenience caused by this issue. We have had some reports of this problem happening in the first OmniGraffle session after applying macOS updates. We are looking for a way to consistently reproduce the issue so that it can be addressed. Quitting and relaunching the application should solve the problem.
If you are in the middle of editing a document, choose Contact Omni under the help menu. Uncheck anonymize data, and attach your document, then change the email from Omni to yourself. That will email your work to the address chosen. Once you have received your document, quit OmniGraffle and relaunch. If relaunching does not resolve the issue, or if this happens at a time other than after applying macOS updates, please contact us so that we can suggest more detailed troubleshooting steps.