We've posted a couple articles on our site to hopefully give readers some ideas of what to do when the index is not helpful and you are "certain" the person is in there:
The second article discusses why I think an 1893 birth record for an individual named Eliney is actually supposed to be Frederick.
Does it look like Frederick to you?The article also discusses how the error likely happened. Sometimes this cannot be determined, but if the genealogist can figure out "why" or reasonably explain the error, it helps to make the case.