Something wrong has happened. You shouldn't see that error message.
I would contact Wolfram Technical Support (https://www.wolfram.com/support/contact/)
Most likely, however, you can fix whatever happened by yourself. Evaluate:
ToFileName[{$UserBaseDirectory, "Paclets", "Repository"}]
This will print out a directory. Go to that directory. You can evaluate SystemOpen on it to open to that directory:
SystemOpen[ToFileName[{$UserBaseDirectory, "Paclets", "Repository"}]]
This is where all the paclet stuff is stored. Deleting the folders here will remove all the downloaded paclet information. You can choose to just remove the folders that are about ChemicalData.
Once you've done this, restart Mathematica and try to use ChemicalData again. It should redownload the paclet.