I think WikiTree X put/puts a citation in the old Sources box and nothing in the Notes box. The system would then compile these with:
== Biography ==
Very basic auto bio OR [contents of the Notes box]
== Sources ==
[Contents of the Sources box]
The 'basic' version of the Add Person system now has a Sources box and no Notes box. And the system does the same thing as above, but without the [contents of the Notes box] bit (as there is no Notes box).
I suspect the problem is that you are (or whoever is having this problem is) using the 'Advanced' option which was added to let people write a bio before creating the profile, and which has the Biography and Sources headings. Then, WikiTree X is overwriting these headings with the citation. I think the solution may be to switch off the 'Advanced' mode for profile creation. (If I've missed something obvious or just misunderstood the situation, let me know.)
Edit: I think I did miss something: the 'Facts'. I think WikiTree X put these in the Notes box, but now, there's no Notes box, so these have nowhere to go.
I think your only real solution if you want to continue using WikiTree X is to contact the author and ask him very nicely to update it, which, I've heard, is unlikely to happen.
Edit 2: I may be wrong again. There may be another option. The WBE has an Add Person Redesign feature, an attempt to restore the old look of the page for those people who prefer it as it was before. If we just add the Notes box back into the page, you won't need the 'Advanced' option (unless you want to add categories or category information boxes). I think using the Advanced option and WikiTree X is causing the trouble (and thinking about it, you'll probably get the same results with the BEE at the moment, which I hadn't thought about...). Restoring the Notes box and not using the Advanced option may allow people to continue using WikiTree X without getting into trouble. (This (restoring the Notes box) is doable, in case you were wondering.)
Edit 3: I've restored the Notes box as part of the 'Add additional fields' option of the Add Person Redesign feature.