Susan Browning and Elaine Stritch being nominated in leading for Company, and Nancy Opel being nominated in leading for Urinetown could also be added. This has happened in some seasons where there were not enough performers in leading roles whom the nominating committee considered worthy of a nomination to fill out the number of nominees considered an acceptable minimum. Other times that may not have been the reason. Still, all of those people (and Palmer) clearly did not belong in leading.
There have been times when people who might well have been plausibly nominated were not in favor of people who did not belong there.