These glitches have become quite infamous, at least to me. If a creation used in a save file in Spore gets automatically shared to the Spore servers, then by my experience, it wasn't actually shared onto the servers. Since you used the in-game model of your empire's species in your adventure, then the adventure likely won't work.
Luckily, there are some workarounds. First, there's a website called Sporistics
, which allows you to look at additional information on creations and adventures. What you'll want to do is search for your adventure, then select Analysis, which will allow you to find a complete list of the PNG files of every creation in the adventure, including those which were deleted, which may then be copied onto your computer and manually dragged into Spore, allowing access to the creations if they're not available online, yet in an adventure which is online.
But as people likely won't know or bother to go through the effort of doing that, what you'll have to do is identify the creations not on the Spore server, go into the editor and save each creation again, (This may require one or more edits, but they can be undone.) release the doubled creations online yourself, then replace the originals in the adventure and upload that edit of the adventure.
If you don't want the original upload online after that, you can log onto the Spore website and delete it there from the online Sporepedia.