Most research articles consist of a Title page, Abstract, Introduction, Methods, Results, Discussion and References. Many medical journals want abstracts with subheadings. Read more
Penelope relies on being able to find these headings in order to carry out subsequent checks. If your manuscript does have those headings but Penelope can't find them, try removing formatting and line numbers.
For some article types, like meta-analyses, case reports or letters, Penelope expects a different structure. You can tell Penelope what kind of manuscript you are submitting by answering questions during upload.