The water, and why hard water darkens a jar
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What the minerals do
Iron in particular reacts with compounds in the spices and the vegetable to produce darkening, and the result is uneven rather than uniform, which is what makes it read as a fault rather than as a style. It is cosmetic and it is the kind of cosmetic problem that stops a jar selling.
Finding out whether yours is hard
Your water supplier publishes a report and it is free. That is a better starting point than a test kit, because it tells you what is in the supply rather than what is in one glass, and hardness varies by area far more than most people assume. If you are on a well, test it, because nobody else has.
What to do about it
Soft water is the straightforward answer and distilled water is the certain one, which matters more at commercial volume than at home because a batch that darkens is a batch you cannot sell. Treating this as an input cost rather than an inconvenience is the right framing once you are making enough to care.
Why it shows up more in some products
Pale vegetables show it and dark ones hide it, so the same water produces a visible problem in a cauliflower pickle and no visible problem in a beetroot one. If you make a range, the pale products are the ones that tell you whether your water is a problem.
Which makes a pale product a useful test batch early on. Make one jar of something light before committing a season to a recipe, and look at it after a month rather than on the day.