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Like the question says so please correct my any of my understanding of how breeding to get perfect IVs work

When two Pokemon are bred, three IVs are passed down to the child from the combined pool of twelve IVs of both parents while the other three are random. If one of the parents is holding a destiny knot, it will instead inherit five IVs from the same pool of twelve while one is random

If that is the case, if you breed two Pokemon with perfect IVs, the offspring would be one with five perfect IVs, six if you're lucky

I was breeding my five perfect IVs Gible with a six perfect IVs Ditto. I hatched five eggs because I wanted both of its abilities. So my question is, how come three of those Gible eggs didn't have five IVs? Shouldn't it inherit at least four perfect IVs? Two of the ones I mentioned only had three perfect IVs while the other one had four

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Were the parents born with that many perfect IVs, or were they hyper trained?
This was oras so they were not hyper trained. One of the parents was 6 IV Ditto and the other was a 5 IV Gible

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First, a random IV is passed from one of the parents to the baby. Afterwards, a random IV of any stat (other than HP) is passed from either parent to the baby; if it is the same stat (not necessarily the same IV value, depending on whether or not the same parent passed it on), it will override it. Finally, another random IV of any stat other than HP and Defense is passed from one of the parents to the baby; this IV will override any of the previous two if it is from the same stat. The remaining stats (a number ranging from 3 to 5) are determined at random, again with the possibility of one or more IVs coinciding with those of the parents.

This has remained relatively unchanged other than stuff like Destiny Knot and Everstone effecting breeding.

Your Pokémon can inherit the same IV twice (picking both the father and the mother's Speed IV, for example), which will result in only having 5 - (duplicate) stats. It is also much harder to inherit HP and Def due to the ways stats are picked. :P

It is possible to have up to two duplicates with destiny Knot, meaning if you have both parents with 6 IV's, it is still possible to breed an offspring with only 3 Perfect IVs. Also, in your case, Picking the one imperfect stat will generate one less IV unless the random stat is rolled as 31, ignoring picking duplicate stats. In your case, the minimum perfect IVs is 2. :P

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Hope I helped!

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I see. So this was not a glitch that I got a couple three IVs
Bulbapedia doesn't say that the destiny knot can pick the same stat twice. Where did you get that information?
In my experience of hatching 350+ eggs in Sun from two 6iv Charmander with a Destiny Knot, every single Charmander hatched had at least 5 perfect IVs. So this answer is not entirely correctamundo.