You're not doing anything wrong. The gods of RNG are just not feeling in the mood for you at the moment.
The way IV breeding works with the Destiny Knot is a little wonky to understand. Basically, when using the Destiny Knot, the game will look at all 12 IVs (6 from each parent) and choose 5 of them of different stats. That particular egg will then have those 5 IVs copied down exactly, with the 6th left to pure random chance. Even if you have both parents with 6 IVs, you are still fighting a 1 in 32 chance of getting that 6th IV to come out a perfect 31.
In your scenario, dad is 31/31/31/31/31/X, while mom is 31/X/31/31/X/31. On any given Destiny Knot pull, you have 3 chances in 12 options of getting a "bad" option on the first pull. The other 4 will depend on whether a "bad" value was pulled, or if it was blocked by that same stat being taken from the other parent. So if Health is taken on the first pull (both at 31), your second pull will be at a 3 in 10 chance (Health no longer valid pull). If Defense is picked (both 31), you now have a 3 in 8 chance (Health and Defense no longer valid). And so on. And after all 5 of those rolls are evaluated, you still have that 1 in 32 chance to get the 6th IV, over which you have no control whatsoever.
The only way to improve your odds is to simply keep hatching eggs until you get a 5 IV female. Alternatively, to obtain a 6 IV Ditto. enter link description here can help you out once they come back online after making their Sun/Moon adjustments. They do have a lot of hoops to jump through to ask for one, but they do run much more lenient giveaways from time to time (more currently, since submissions are down).