Simpler error message dialog
The error dialog is too verbose for an end-user.

Does this only happen in the Server Admin UI? In that tab it was by design - only admins use the admin tab, so I reckoned they should be Ok seeing the full stack trace :) But if one of these dialogs slipped into the diff tab I'll modify. Did you spot any?
I still see lengthy stacks in LogDiff:findBaselineMatches occasionally when bad data causes null pointers
I'd still recommend to use a simpler error dialog to an end-user, including to the admin. I've made a feature request ticket in Protege to have the error dialog be able to collapse or expand the error details (Ref: https://github.com/protegeproject/protege/issues/487). Hope this would fit better.
@bdionne could you post the steps to replicate those NPEs?
The NPEs in LogDiff:findBaselineMatches are detailed here. I can't recall the exact steps, but I was able to somehow create bad data, an annotation change with a null property. You can see in LogDiff:findBaselineMatches where that would cause problems. Not sure whether it's worth putting in defensive code for it or not. I'll keep my eye out for it