It isn't shocking, or unusual
School can plan to complete the spec, but all sorts of things can prevent it
largely, no staffing, teacher absence, no funding for supply staff, school carrying vacancies it can't fill, merging classes, etc
No resources, changed to the spec, that schools can't fund
Poor behaviour, disruptive children - the number of parents that say "they are only a bit chatty, so what" well guess what, it impacts on everybody's education hugely - who'd've thought it!
Students just not working fast enough - not completing homework, lazy, or SEND, term time holidays, absences etc
In may schools, including mine, it is approached differently - we don't plan to finish the spec, knowing we will be unlikely to do so. Instead, we inform students early on which parts of the spec they will be covering independently, so they can make a start on it, and have lesson times to bring up any questions they are struggling with
It is completely normal for some of the spec to be done independently - GCSE students should know what spec they are on for all subjects, and keep track of what has been covered, what they are strong or weak on, and what the school is not covering. The only difference is whether these are planned gaps, or just the gaps left at the end of the course.