When using yEd, it applies some sort of lock to the system clipboard - this is apparent from Excel which gives the prompt (“There's a problem with the clipboard, but you can still paste your content within this workbook.").
I have researched this and am sure that it is not a Microsoft/Excel problem, but consistently occurs when yEd is running with a document open. It can be immediately resolved by closing yEd.
A test to demonstrate the problem: Open both a yEd document and Excel spreadsheet. Select any range of more than one cell in the spreadsheet. Using the mouse, drag the selection to move the cell contents to other cells. The error message will show. If you close yEd and repeat the spreadsheet task, it will work immedately without error.