I think some of the reading level systems like Fountas and Pinnel or Guided Reading take into account the complexity of the text in terms of theme, concepts, vocabulary etc. whereas the lexile system seems more interested in measuring decoding or how difficult a text would be to read fluently. So there may be a certain book that is very simple to read but hard to understand, and those would be given a higher reading level than what it would appear on the surface, or by the lexile value.