Are you using a content type with revisions enabled?
This is incompatible with faceted search which builds it's query on the nid and not on the vid. For example if you edit a node with nid 10 and vid 20 and a term tid 1. A new entry in the term_node table is inserted: nid 10 vid 21 tid 2. The faceted search module will build a query using the nid and tid only. When you filter in your search for the term with tid 1 the module will query on tid 1 and will still find the node with nid 10 but it's the wrong revision of that node.
I didnt had the time to search for a decent solution. I just disabled revisions. If someone has found a way to alter the query let me know contact [3]
Links
[1] https://dominiquedecooman.com/blog-topics/contributed-modules
[2] https://dominiquedecooman.com/blog-topics/search
[3] http://dominiquedecooman.com/contact