The only issue might be, that anyone at the university who does see and read the form in its entirety might wonder which version of the grade is the correct one. And if deciding that the referee's is more likely to be, wonder whether any of the other grades the applicant entered were not what they actually got. They may not be able to do anything now (or even look at their emails for a couple of weeks), but I would suggest that your DS at least emails the teacher who wrote the reference to say that he had asked to see his reference and noticed that there was a discrepancy.
Looking at the publicly accessible area of the UCAS 'Adviser' section, there is an option to indicate that the referee has fully checked the applicant's qualifications and the universities do see whether this box was ticked or not. If it was, then hopefully anyone seeing a lower grade mentioned in the body of the reference would assume a typo on the referee's part, not an attempt to deceive on the part of the applicant.
www.ucas.com/advisers/managing-applications/our-adviser-portal/references-and-predicted-grades#checking-qualifications-
If universities don't distinguish between 8 and 9 anyway(?) it would presumably be less of an issue than an applicant claiming, say, a required 4 in Maths and the reference mentioning them having got a 3.