SQL Server seems to require some files on the C: drive, regardless of what you select.
During installation, you've got the option of where certain things should be stored. If you specified that each location you could specify was on your D: drive, then anything that was placed on your C: drive probably has to be there.
Moving these directories manually is not a good idea; you would need to update the paths the SQL Server engine uses to access those files
Note that shared files are shared amongst different instances on the same machine (at a minimum). If you already have an instance installed, I do not believe that changing to a new directory for shared files when installing an additional instance will update your existing instance(s). Best case scenario, you'll wind up with "shared" files in two different places, not being shared by your instances. Worst case scenario (unlikely, but not necessarily impossible), your existing instance(s) could become non-functional, if they're looking for files in the old location, and the installer has moved them to a new one.