There are some cases, specially if fulltext conditions and aggregation are used, where a query sometimes returns no results even thought with the right index it does return the results. This is a bit hard to understand, because it doesn't match the rule "indexes should only affect performance, not results". One such example is if a query uses one or the other index, but not both. Or if a query uses fulltext conditions on different nodes (parent and child). Examples:
Related is the usage of relative properties in indexes, excluded / included paths.