Fixed in the next release. However, I would be wary of removing languages created by the importer. Doing so may make the translations for some imported pages map to the wrong pages or none at all (if translations were used in VW3).
The VW4 importer tries to use the language code of languages to determine if the target database already contains a language before importing it. It is possible that the default language for XenForo would have had a different language code than the default language for vBulletin 3 (maybe 'en' versus 'en-US'). On the other hand the VW3 importer doesn't use this check, and imports all languages anyway.
I have fixed this for the next release, and fixed a bug in the VW4 importer where colliding language codes don't properly map translations.
In the next release, I have added an option when deleting languages to move all pages in that language to a different language. This should allow admins to fix issues where there are three different languages imported for 'de', 'deu', and 'ger', which are all perfectly valid ISO codes for vanilla German, yet all refer to the same language and should be treated as such in the wiki without losing translation links for each one.
So thanks to this report, 2 bugs have been fixed, including potential import data loss, and the admin tool for removing languages has been improved.