Sorry, but I very rarely fall victim to any conspiracy theory hype. And the victim mentality is very rarely used by those who take responsibility for their actions...
I know of reputable breeders who have had terrible years (this year being one with the very finicky weather - out of 30 mares, I think 2 or 3 are pregnant) however all vaccinate properly and none have had adverse reaction such as limb deformities. However, the breeders I do know who have had limb deformities or other faults in foals outside of the norm, they have all not supplemented mares properly.
Blame the vaccine or look at your program. It's the same as anything in life, in order to be successful we must stay humble and be willing to accept that we may not be perfect, or have the perfect ideas.
They say money doesn't buy happiness -- well happiness doesn't buy horses!