Picard is working as expected. You are putting in CD2 of a two disc set. So Picard loads up the correct match for you. On the right hand side it correctly shows the whole two disc set.
Pop in CD1 and press the button and you’ll find the release will be the same on the right. Again correct behaviour as these two CDs both point to the same release.
When tagging the files, if you only have the files from CD2 then will match the bottom half of the right hand side. Lining up alongside tracks 2-01 to 2-14.
Add the files from CD1 and they will now line up with the top half - tracks 1-01 to 1-24.
You have not damaged the database. It seems to all be working as expected. A multi-disc release will always bring all of the discs into Picard. This is a database of releases as you would find in the shop. It is not a database of individual CDs.