I assume that we do not know the meaning of every single word attested in classical and older Latin (literature, inscriptions, and other material). If this assumption is false, it makes this question pointless, but a well explained justification of it would constitute a good answer.
It seems fair to assume that in general rarer words are not known as well as more common ones. Therefore many unknown words are probably hapax legomena. But are there more commonly occurring words whose meaning we don't know? In particular, what are the most common Latin words that we don't understand?
Understanding the meaning of a word is non-binary: there is a lot of room between understanding fully and knowing nothing at all. Any suggestions of poorly understood words, particularly ones occurring several times, are welcome as answers1. Also words that have only recently been figured out are interesting. Also, the frequency of a word depends on the corpus used, but that should not invalidate the question. Instead of trying to give too stringent definitions, I trust you to make a judgement call.
Let me exclude names from this question, since their origins are often unclear and meaning (if any) is secondary to their use.
1 If you know a suitable word, please suggest it as an answer since it is an answer. Comments are meant for clarifying and improving the question or making related remarks, not for answers. If you can't give all the details you wanted to, perhaps someone else can help you.