One bug in GEDCOM Analyzer is that a CHANge record corrupts the displayed death date (with the Change date).

Another issue is that if two people have the same name (eg from different generations), the cross-file comparison shows miscompares between the different people, even though the corresponding people's entries match.

In any case, it is hard to get a good overview of how two GEDCOMs differ when they are from totally disparate sources (even when they cover mostly the same people).