That's expected behavior. The commenting tools can not interact with data in the form fields, only with static content on the page.
When I emailed my professor about this issue his reply was "Hi, We have had more than 1,000 students over ten years do these assignments in PDF format. You can do it just like others. It isn’t that complicated." Surely there has to be some way to highlight this text in the document. That seems like very basic functionality and if "more than 1000 students over ten years" have handed in this assignment I'm sure there has got to be a workaround.
Sorry, but they're wrong, or you're talking about two different things.
The only workaround is to flatten the form fields and convert them to static content. Then you'll be able to use the highlight (and other) commenting tools on them.
Did you create the form fields?
Is it possible that the sequences to be added were put into comment text boxes and not form fields?
If is possible to make the form fields to be set to "Rich Text" and then color the font for strings within the form field.
If I select the comment tool and start outside the field, I can have the highlight the field or part of the field. So I could start the highlight above and text in the field I want to highlight and stroke down to cover the text I want to highlight.