Lose the fruit puree & switch to natural flavors.
Switch from Apple Pectin to Citrus Pectin. Apple Pectin is not recommended for gummies.
Then I would imagine you are getting the occasional clump, or probably more likely – your consumers’ physiology is just more susceptible to stronger effects than usual here & there. Consequence of offering what I would consider an irresponsibly high dose.
That math checks out on a basic level if there is no excess slurry & no shortage of slurry – makes 500 exact.
Side note: 1g does not typically equal 1ml with gummy slurry.
Tough w/ puree & apple pectin.
Use HM slow set 60-65 ester pectin. Sodium citrate to stop pre-gel. Crank temp up 10-15 degrees when you add citric. Heat your molds in oven before laying them out. Use lowest citric acid concentration you can to achieve gel. More sucrose, less glucose.
Great Atago refractometers are ~$250 & well worth it. Get one that can properly measure in the 70’s & 80’s SS range & at high enough temps.
Water Activity. Package below .65 AW. If you package above .7 AW, they will mold. AW meters are ~$5k-$6k.
Can get by without – if gummies get moist after sealing, you see droplets on sides of containers, sugar coating melts into gummy… you are at risk of mold. Unseal, re-sugar, and dry some more.
It can vary within the liter. Probably not enough to be the source of this issue. Certainly varies within the batch. Still probably not the source of your issue.
Another note.
I’m guessing you aren’t using a PH meter. You will want one for sure. Target PH depends on brix you pour at & sugar makeup, among other smaller factors.
Generally 3.2 - 3.6