Apple’s mbox files are non standard mbox files. Thunderbird cannot import these. Only Apple Mail can read these .mbox files.
The easiest way is to have Thunderbird simply import from Apple Mail. It’s unclear what happened when you selected the import directly from Apple Mail.
Or you can go for application use. There are a lot of third party tools which deal in mail migration issues. One such application having expertise in migrating emails from apple mail to thunderbird is Mail Exporter Pro. Have a look at the following link:-
http://mailexporterpro.com/export-emails-apple-mail-to-thunderbird.html