Are you controlling the text by means of a paragraph style? You can setup both hyphenation and justification settings inside the paragraph style, apply it to the text, and see if it changes what you are seeing.
You might also take note of what language the paragraph style is set to.
Thank you. I'd had trouble with style sheets since new CC/Typekit, and ended up doing way too much manually. Looks like it was cleared up by style sheet/hyphenation.