I see some issues with the question. One of them is the unclear problem statement, since the question seems to contain three different ones:
What is the "preferred way" of storing small sets of data in Java?
Why does the "Yaml library from Bungeecord" has sometimes loading errors / how can I deal with them?
Is there another, more stable Yaml library for Java?
Asking three questions in one alone can lead to closage with the predefined "needs more focus" reason. Sometimes, these kind of question can be salvaged by removing off-topic parts from the post and keeping the rest. However, I think in this case this won't work, since all three questions are not suitable for Softwareengineering.SE:
Ad 1: There is no "preferred way", especially not in the Java world. There are virtually dozens of ways how to store such data, but which to use is heavily opinionated. Sure, some of those ways may be better suited for your requirements than others, but in the end, it boils down to the taste and knowledge of the programmer.
Ad 2: That could be a good one for Stackoverflow, but not Softwareengineering, since we don't give debugging help here. However, Stackoverflow will only accept such questions when they contain a short code example to give others a chance to reproduce the problem.
Ad 3: Questions asking for library recommendations are explicitly off-topic for this site, and the same holds for Stackoverflow (though, like in this case, one can sometimes find some answer there, either). Today, Softwarerecs.SE is the most suitable place for such questions. Often however, it will be quicker when you simply google for "yaml java libs" (that's how I found the link to SO from above).
Since your question was already deleted, I would recommend you forget about #1, ask a proper question about #2 at Stackoverflow (with some example code), and if you want to try out a different lib (#3), start with the ones suggested among the answers behind the link to Stackoverflow I gave you above. And in the unlikely case that none of the libs will suit your needs, ask a question about it on Softwarerecs.