When a user selects more than one row I check if all rows have the same features. Otherwise I show an errordialog.

this behavour is not very usefull for a good UX

Opening an error dialog on selection is good UX? Another good example for different opinions on good UX. But that's a different discussion.

You need to tell me how you perform the multi selection. Drag selection? Ctrl + left click? Key movement?

After some further investigation, the issue is that opening the message dialog prevents the NatTable internal event handling from processing. So the drag mode is activated after the dialog is closed, although it shouldn't have. But the mouseUp event was not able to get handled correctly, since the processing was stopped and the mouse event handling is activated afterwards.

I have no idea how to fix this internally, but you are able to deal with it if you open the dialog asynchronously. This way you don't stop the internal NatTable handling and everything works as intended.

Display.getDefault().asyncExec(new Runnable() {

                            @Override
                            public void run() {
                                MessageDialog.openConfirm(Display.getDefault().getActiveShell(), "Interrupt", "Interrupt selection");
                            }
                        });