Short fragments (< 100bp) represent chromatin-free regions and should be retained. Those are regions that most likely are actively transcribed since they are accessible to transcription factors (TFs) and polymerase complexes.
Larger fragments can also appear with a periodicity of ~200 base pairs and indicate mono-, di-, tri- nucleosomes. Those can be excluded or used to infer nucleosome positions. Larger fragments are excluded because they do not truly represent open chromatin regions between histones.