One early guess about these holes is that another T. rex bit Sue here. It seems like a reasonable guess; the size and position of Tyrannosaur teeth about match up with the series of holes. Several scientists, including Ewan D.S. Wolff of the University of Wisconsin-Madison and Steven W. Salisbury of the University of Queensland, Australia, felt there was something "off" about that explanation. If these holes, and similar lesions on other Tyrannosaur jaws, were bite marks, they should be more ragged, and the jaw would appear more crushed. Also, bite marks were rarely consistent between specimens; however, the holes in the T. rex jaws were very consistent. They turned to a more mundane explanation.
In modern raptors, there is a parasite that causes something called trichomonosis. It attacks the jaw of these raptors, leaving a pattern of lesions that is very similar to that on the Tyrannosaur jaws. The scientists now suspect that the trichomonosis parasite, or something similar, was passed within Tyrannosaurs (there is no evidence of the disease in other dinosaurs). These creatures were known to attack, and even cannabalize each other, so the parasite could spread easily.
In Sue, the infection was very severe to drill holes in the jaw. It would have also created a film across the back of the dinosaur's throat. This would have made it very difficult for Sue to eat. This parasite could have easily lead to Sue's death, by starvation.
Credit: Science Daily: Was the Mighty T. Rex 'Sue' Felled By A Lowly Parasite?
See the Field Museum site for more information about Sue.