Are you using the same brass as listed in the manual? If the brass is thicker there will be less internal volume. If the brass is thinner there will be more internal volume. Different brands of brass and even different lots from the same manufacturer can be somewhat different. If your load becomes compressed but isn't listed as a compressed load in the manual then you probably have brass with a smaller internal volume. That also means you will probably have higher pressure and velocity than the numbers published in the book. You will probably reach max pressure/max velocity with a given powder before you reach the max load in the manual.
There is nothing wrong with using thicker brass, that is why you need to do load development with a fixed set of components in a specific rifle. There are many variables that will be different with your setup than what was used in the lab when they developed the load data.
Keep as many things consistent as you can, develop your load, find whatever you are looking for (optimum accuracy or max velocity), and keep loading without changing any variables. Many shooters weight sort their brass for higher consistency. Brass should have a similar density so a heavier case will contain more brass. If the external dimensions are the same that means there must be reduced internal capacity if there is more brass. In 308 for example one brand to another could have a weight difference of 20+ grains. That means there is 20 grains more or less worth of brass inside the case.
You could also do water tests to check capacity or use some sort of consistent fine powder.
