What bullets are you using? A certain amount of seating depth variance as determined by cartridge base-to-ogive (CBTO) can be caused by variance in bullet external dimensions. Sorting bullets base-to-ogive with calipers into length groups, or sorting using a tool such as Bob Green's comparator will largely solve this problem.
Alternatively, a certain amount of seating depth variance is not unexpected, even when using length-sorted bullets. However, it should be more on the order of +/- .001" or maybe .002", not .009". I use a target CBTO range for loaded rounds of .0005". For example, I might want an "acceptable" CBTO range of 2.2000" to 2.1995" for a loaded round. I set the die micrometer such that most (70-90%) of the loaded rounds will measure exactly 2.2000" with a single pull of the press handle. The few that might be out of the "acceptable" range will actually be long by half a thousandth (i.e. 2.2005") as measured by the calipers. It usually only takes another pull of the press handle (i.e. an extra "tap") to bring them into the desired seating depth range. This usually prevents any rounds from ever being seated deeper than intended. However, it does require that you measure each loaded round, which I do.
Another potential source of seating depth variance is non-uniform neck tension. Are you annealing your brass every firing? It can make a difference. More often than not, you can "feel" rounds that end up seated longer than desired through the press handle; they seem to seat harder, with a bit more effort, suggesting greater than average neck tension. A seating die that measures seating force is one way to quantify this issue, but potentially comes at the price of having to buy additional equipment. I usually set aside rounds that "feel" like they seated noticeably harder than the others as foulers/sighters, even if they seat within my chosen acceptable CBTO range, as they are likely to have greater neck tension, which can affect velocity and precision.
The bottom line is that .009" CBTO variance is pretty high. Identifying the underlying cause is the most expedient way to solve this issue. However, even if you can't identify a specific cause, you can usually improve the seating depth variance using some version of the method(s) I described above. In a worse case scenario, you may actually have to re-adjust the die micrometer for rounds that end up longer than desired. That is a process I find to be a PITA, but again, necessary if you want consistent very seating depth - something I feel is essential for good precision. As I mentioned, you have to measure every loaded round to be sure. As long as none are shorter than the desired CBTO, you can give them another tap in the seating die, or even adjust the mic, if necessary, to get them where you want them. But in order to do that, you need to know the CBTO measurement. It does take a little more time, but having measured every seated round for years, it is now habit for me to use the calipers as I seat each bullet.