The Single Transferable Vote system was specifically designed to handle this situation. A low keep-factor on several candidates means that it was a very good decision to use the STV system for this election.
In STV, the voters can usually rank as many candidates as they want. There are multiple variants of how to count votes in an STV elections, but usually the situation in which a vote gets completely wasted is when all the candidates on a ballot reached the election threshold. The voter said "I want B, D and F, and nobody else" and that's exactly how their vote got interpreted by the system.
There are also counting variants where the votes of an eliminated candidate can not go to another eliminated candidate, so that's another way how votes can get discarded. When a lot of votes get discarded that way, it might be worth analyzing why some options appear very frequently on lower ranks but very rarely on higher ranks. Whether or not this is good or bad depends on circumstances and opinion.
In a non-transferable vote system, a very popular option often takes away votes from very similar options (the spoiler-effect) which results in the mainstream opinion being under-represented in the resulting parliament. But in a transferable system, people who vote popular options can still set the similar options as alternative choices, so these similar options aren't punished for following the mainstream opinion. This also limits tactical voting (I like all vowels, but I like A the most. But A is so popular they get over the threshold anyway, so I am dishonestly voting for E hoping to get a second vowel into the parliament).
For further watching I recommend the video "Politics in the Animal Kingdom: Single Transferable Vote" by CGP Grey.
But all of that only works properly when you allow voters to rank as many candidates as they like. When the number of ranks is artificially limited in your STV election and a large number of votes go to waste although they used all allowed ranks, then that's a sign that the number of ranks might have been inadequate to allow these voters to properly express their opinion and that it should be increased.