Think about your own reading experiences. When you have to stop reading to go back over an incomplete or badly structured sentence, you lose momentum. Likewise, when you have to re-read sentences to track pronoun references or subject-verb agreement, you can lose the thread of the text as a whole. Thus, sentence structure errors tend to be at the top of most hierarchies of confusing errors. These problems are closely followed by faulty pronoun reference and subject-verb disagreements.
Those errors that are less and less noticeable usually fall at the bottom of the hierarchy. For many readers, these errors don't even slow down readers. Sometimes, surprising errors fall into this category. As we have become more and more accustomed to following a singular noun with a gender neutral pronoun (the student....they), many readers skip right over the pronoun agreement error that would have stopped readers in their track 60 years ago. Similarly, as more and more publications lose track of correct use of apostrophes to mark possession, most readers don't even notice missing apostrophes.
In creating your own hierarchy of errors, you should probably tell students your ranking criteria - potential to confuse readers, strict grammatical correctness, ease of reading, and so on.