Chain not sliding into casette perfectly
By definition, if the chain is not running on all cassette sprockets properly, the indexing and/or limits are not properly adjusted. Low limit setting being off would be my guess.

Run through the full indexing adjustment procedure. Park Tool Company has the best instruction video. 

You can check the derailleur hanger by lifting up the rear wheel and looking down a line from the derailleur cage to the chainrings. The cage should look parallel to the rings.