This is a normal styling convention that book designers use when typesetting manuscripts. The first paragraph of a chapter or section is generally styled using "body full-out", meaning that the first line is not indented. This is standard in publishing, and leads to a much tidier look.
If you're not satisfied with this convention, however, our designers can style the paragraphs however you'd like. Simply indicate your preferred styling among your interior revisions to be submitted through Octavo.
Note, if requesting a change to be made everywhere in the book, you only need to request the change once, the first time it appears in the draft. Just make sure you specify in the revision comment that the change is universal, to be implemented everywhere in book.