There are a few that come to mind as one that have an obvious explanation. One is the sinistral species of Busycon (whatever Petuch, Hollister, and the like have said about generic assignment). The flip in coiling direction is known to be a very rare (usually) mutation in most snails. A few groups are normally sinistral (e.g. Planorbidae, Physidae, and Triphorinae), and a few random species elsewhere are consistently sinistral. The main point is that sinistral individuals can only mate with other sinistral individuals. Hence, as soon as a population appears, it could be considered a separate species (assuming that sinistrality is rare). Eventually, they may diverge noticeably from their dextral counterparts.
Another set of cases are groups that have so few fossil occurrences that trying to draw any hard conclusions about when they appear is impossible. Examples include Tjaernoeia (of which the only known fossil is sitting in a vial in my collection), and the family Cornirostridae (which have virtually always been put in other groups). It helps if the organisms’ remains are very similar to those of other groups, and are also tiny. [let me clarify-the largest specimens known of those two groups are about 2.5 mm across]