If the answer is yes then although it appears that your department has not taken into consideration the circumstances do not worry - departments normally like to see how you progress in the final year of your degree and then consider all the evidence when considering your degree classification. For example if you do well in the final year but your marks from the second drag the marks down then they will look very closely at the circumstances that occurred in the second year when considering which degree classification to award.
If the answer is no then it is not to late to submit an account of the circumstances alongside supplementary evidence to your department. They can then consider the problems when considering which degree class to award you at the end of your course.