It is really important that you keep the joins in the blades clear of fabric. If you use the die a lot and don't clean, built up threads could force the blades further apart, making the problem worse. I use a stiletto.
Also, just as a well used cutting mat will cause skips in your cutting, the accuquilt mat will develop grooves & need to be replaced. When you are at this point, there usually are multiple areas that are roughly cut.
The dies are made from sharpened steel rules, which as their name implies are just long strips of metal. They are bent to shape and then embedded in a plastic or wood backing. There is always one or more points where the steel meets itself, like if you took a strip of paper & made a circle. Sometimes the gap is a bit bigger than it should be and it will leave more than a thread or two uncut. This is not going to fix itself and if it really bothers you, you could contact them to exchange it, but the exchanged die may be the same.