Your source files have different numbers of dipoles = your cortex surfaces have different numbers of vertices.
If you are using individual brain scans and not anatomy templates, then the cortex surfaces don't match and you need to project them onto a template before any group analysis.
- https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects
- https://neuroimage.usc.edu/brainstorm/Tutorials/Workflows#Average:_Group_analysis
- https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup#Project_sources_on_template
With the files you sent me, it is not possible that the output of the "Difference of average" was correct. You probably had similar warnings or errors generated on the way.