Comprehend doesn't support overlapping annotations, i.e. when a section of your text is annotated twice. Make sure the annotation is correct in the line that Comprehend found the error. If your annotation is correct and you have frequent overlaps in your document then creating two separate models is the suggested workaround.
If you are using a custom entity file (as opposed to an annotation file), you cannot have an entity term be the same or a substring of another entity term. For example if you have one entity term that's "login" and another that's "user login" belonging to different entities, the auto-annotation will then overlap as it's trying to annotate the overlapping substring "login" to 2 different entities.
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