You can only craft flawed and cracked stones by failing your check
This is was explained on the Ioun Stone creation process on Seekers of Secrets (pg. 43 and 44), more specifically, under Cursed Ioun Stones:
When a magic item creation skill check to create an ioun stone fails by 5 or more but less than 15, there is a 50% chance the result is a cracked stone and a 50% chance the result is a flawed stone. If the check fails by 15 or more, the stone is actually cursed;
Other than that, you cannot try to create them on purpose, they are the result of failed experiments. The cost to create them, however, is the exact same of creating the perfect stone.
Crafting requirements can be ignored
With the exception of the item creation crafting feats, all other requirements can be ignored if you increase the skill check DC by 5 per requirement, even if that requirement is a minimum caster level as was noted by this FAQ:
Though the listed Caster Level for a pearl of power is 17th, that caster level is not part of the Requirements listing for that item. Therefore, the only caster level requirement for a pearl of power is the character has to be able to cast spells of the desired level.
So, for our Dusty Rose, the DC is 17 (5+item's CL of 12) if you have all requirements, or DC 22 if you do not possess a caster level 12.
As you might have noticed, the easiest way to fail and produce an inferior ioun stone is to purposely increase the DC and try to fail on your check.
If you really want one of those, you could craft the stone in combination with a lower level caster that does not possess the feat, so they will have to make the check with the increased DC. This assumes you are also not at caster level 12. Otherwise, you will fulfill that requirement and the DC decreases back to 17.
It is possible for more than one character to cooperate in the creation of an item, with each participant providing one or more of the prerequisites. In some cases, cooperation may even be necessary.
If two or more characters cooperate to create an item, they must agree among themselves who will be considered the creator for the purpose of determinations where the creator’s level must be known.
Should that scenario become impossible, try to find a caster with the feat and let them create it. Casting Bestow Curse or similar long-term debuffs is probably the easiest way to guarantee the creation of failed stones, but basically, you just need that their total skill check cannot hit 22 even on a natural 20.
Finally, just like in D&D 3.5, you may also Take 10 on the skill check to create magic items in Pathfinder (as seen in this answer). This means that failing on purpose is even easier, you just gotta make sure your total bonus is +11 or less, but still above -3 so you don't produce a cursed stone. From there, it's a gamble between flawed or cracked stones (50% of each).
Also, before you try this, see this answer about trying to intentionally fail a skill check and consult if that's ok with your GM. Some GM's are not really fine with players trying to sabbotage the rules by manipulating check results and might ask you to roll for that check even if taking 10 would be allowed.