to backfill missing episodes
a) go to the Wanted page, select the missing episodes, click on the Search Selected button
b) open the Series, click on the episode title, change to search tab, click on Automatic - repeat for each missing episode
if sonarr downloads something and then it sits waiting for manual import and has a red exclamation mark and episode/file missing reason then its usually because the torrent/nzb was fake and there just an exe file or some other crap in there - in which case just delete the job and blacklist the download. sonarr will then go search for it again.
you can always check what files are in your download clients completed folder if you want to know why sonarr cant import it