Same here, I had put my Nautilus Fossil and Amphibian Fossil in the museum, but on my collection page it did not show it was collected.
I have collected new Amphibian Fossil and museum won’t allow me to put new amphibian Fossil in because there is old one already in the museum.
Now, I also just got 2 new Prehistoric Ribs from T-Rex in skulls cave, prehistoric floor. I have not put 2 prehistoric ribs in the museum yet and on my artifacts collection page it show that I got 2 ribs
The artifacts page has nothing to do with the museum.
Artifacts (and minerals) page only show you what you found. You can donate only one of each.
There is a known bug where sometimes the things you find don't show up on that page immediately, so you might wanna check before donating to the museum. Putting it in a chest and picking it back up or sleeping with it in inventory might solve that.