All honesty, I don't know this story, so anyone who does should correct me. However, I think your perception is that there are many different enanthate and cypionate batches being produced and sold. I think the truth is closer to the idea that one massive batch of enanthate that makes up the majority of the "raw" ester that's around. People buy and prepare it in oils and distribute it, but the source for most of them is either the same batch or a common manufacturing process. I don't know why the enanthate would have an issue that cypionate doesn't, which may (again) reflect one batch that had an oopsie, or one process that hasn't been ironed out.
Chemically speaking, esterification reactions can involved some pretty nasty reagents. Even very simple reactions, like making a methyl ester from a simple carboxylic acid, involves acidified alcohol that reacts violently with water. If any of that reagent is not fully evaporated, I'd expect it to be quite unpleasant to put into your flesh.
Like T&H said, the prices for enanthate are better on a per-molecule basis... the ester weighs pretty much the same, the concentration is higher, and the vials tend to be the same price. I don't know how the pip is for modern enanthate, but people tolerate shit like DHB and aqueous suspensions, so it seems like there's a huge variety in the amount of misery people are willing to accept.