You must specify the required Version compatibility when creating a NGramTokenFilter. As of Lucene 4.4, this token filters:
- handles supplementary characters correctly,
- emits all n-grams for the same token at the same position,
- does not modify offsets,
- sorts n-grams by their offset in the original token first, then increasing length (meaning that "abc" will give "a", "ab", "abc", "b", "bc", "c").
You can make this filter use the old behavior by providing a version < Version#LUCENE_44 in the constructor but this is not recommended as it will lead to broken TokenStreams that will cause highlighting bugs.
If you were using this TokenFilter to perform partial highlighting, this won't work anymore since this filter doesn't update offsets. You should modify your analysis chain to use NGramTokenizer, and potentially override NGramTokenizer#isTokenChar(int) to perform pre-tokenization.