Typos that lead to misspellings, a misplaced comma, a wrong word, for example, can be pointed out and a student can be instructed to fix them on a final draft. Run-on sentences, however, can't all be remedied as easily. The writer needs to think about the sentences and needs to decide what is the best way to fix it. If so, what kind of coordination should exist between them. Where does the sentence fit in the paragraph, and where does the paragraph fit in the paper at large.
Some sentences fall apart because a writer jumps thoughts in mid-sentence.
Correcting for these matters often cannot be addressed by pointing to a usage or grammar rule. Often it's a matter of talking to the writer about what he or she wants to say, asking them to clarify their thoughts a bit first, and then showing them the different ways they can make the changes. Changes in grammar, punctuation, usage, and yes, even mechanics and layout are not trivial matters. They do affect how people read and perceive both the prose at hand the writer. However, precisely because they are not trivial, they cannot be handled as matters of right or wrong, correct or incorrect, rule bound and gagged.