You will want to first go into Song>>Song Setup>I/O Setup and verify that your input ports are configured correctly. You will also want to check that you have the correct input selected for the track that you are recording to.
As a possible workaround to the issue, you can try creating an aggregate device on your Mac that includes the Apogee Mic and then set the aggregate device as your input and output. Make sure that you go into the I/O setup and configure the input ports as desired. Here is an article from Apple that explains how to create an aggregate device...
For general troubleshooting inside of Studio One, you can try removing your settings files and re-configure. Here are instructions:
1. Go to Help>Open Settings folder.
2. Copy the contents of the folder over to a folder on your desktop.
3. Close S1 and delete the contents of the settings folder with the exception of the user.license file as well as the "Extensions" folder.
4. Open S1 and go to Studio One>Options (Preferences on a Mac) to reconfigure your settings.
5. Test to see if the problem is resolved. If it is not, please feel free to copy your settings files back over from the backup that you created in step 2.
*If you are missing presets or Sound Sets after doing this, simply double-click one of your Sound Sets under Documents>Studio One>Sound Sets.
You may also want to try reaching out to Apogee on the issue. They may know of a workaround or have some additional information for you.