Yes, but this is a completely different story, because it is vaccine proponents and not vaccine antagonists who are citing the issue — duh! Medical school textbooks and pro-vaccine poster child Paul Offit also recognize this issue as well as the CDC.

Full paper (Fine and Chen): Confounding in studies of adverse reactions to vaccines
This paper has a correction: http://aje.oxfordjournals.org/content/136/8/1039

CDC researchers Fine and Chen are obviously deeply concerned about HUB, and the implications for the reliability of vaccine safety studies. They state that studies are not “useful” unless HUB is controlled. In view of these concerns, it’s alarming that vaccine safety studies typically ignore healthy user bias altogether. They almost never make any effort whatsoever to control for it.

Vaccine promoters acknowledge HUB. For example, the most widely used textbook on vaccines by Plotkin, Orenstein and Offit (yes, that Offit) states the following:

“Confounding by contraindication is especially problematic for non-experimental designs. Specifically, individuals who do not receive vaccine (e.g., because of a chronic or transient medical contraindication or low socioeconomic group) may have a different risk for an adverse event than vaccinated individuals (e.g., background rates of seizures or sudden infant death syndrome may be higher in the unvaccinated). Therefore, direct comparisons of vaccinated and unvaccinated children is often inherently confounded and teasing this issue out requires understanding of the complex interactions of multiple, poorly quantified factors.” (Emphasis added)
–Vaccines, 5th ed, 2008, page 1631

I get that this is sending you into serious cognitive dissonance land, but sorry, that’s the price of actual science and not blind dogma.