I’ve looked around the forum and I’ve found a few posts of people having the same problem. Many of the files are only partial files after being processed and moved to the proper folder. From what I’ve read this may be a problem with zip files and that Sonarr moves the file while it is still being actively extracted and so only part of the file is moved. Or may also be an issue with cifs/samba shares. I cannot change my shares to nfs because my Windows machine (Windows 7 Home Premium) does not support nfs.
The actual media files are located on a linux machine, but I use my Windows 7 machine for daily use and it is what I use to manually download movies and sometimes tv shows, so I still need access to the shares on the linux machine. But I have Sonarr running on a Raspberry Pi, mainly because I’m not very experienced with linux and so if I break something while running/installing/modifying Sonarr I can easily just wipe the whole thing and start over.
If you absolutely want Sonarr on the rpi, consider using sshfs on your PI, or nfs complementary to the existing samba/CIFS share. They aren’t mutually exclusive.
Installing it on your linux server is probably still the best way, performance wise as well.