The situation of having only one Cylon in a 5/6 player game is possible if using the Exodus rules for execution and loyalty deck setup. The Exodus expansion added the concept of "You are not a Cylon" deck in addition to the Loyalty deck, and also an additional step to Human Execution:
The player adds one card from the “You Are Not a Cylon” deck to the
Loyalty deck, shuffles the Loyalty deck thoroughly, and draws one new
Loyalty Card,which is kept hidden from the other players.
In addition, the loyalty deck rules for Exodus always leave one extra card in the loyalty deck, after all of the loyalty cards have been dealt in the Sleep Agent phase. This occurs even if playing with other expansions.
This is done in order to prevent the certainty that comes after executing a character. In the original Pegasus execution rules, executing a character meant knowing for sure whether this character is a Human or a Cylon. In the revised Exodus rules, this means that executing a Human character might turn this character into a Cylon. It does mean, however, that in a five player game, where we have 2 "You are a Cylon" and 9 "You are not a Cylon" cards in the loyalty deck, the chances of one of the "You are a Cylon" card to be at the bottom of the deck are 18% (16% in a six-player game), and thus that card won't be drawn at the sleeper agent phase.
Each execution or personal goal revealed before travel distance is 6 adds an additional card to the Loyalty deck and mixes them before dealing a new Loyalty card to the player who got executed or fulfilled a personal goal, so this probability drops down by 50% each time this happens. Even then, this means that the second Cylon can enter the game only after significant amount of time.
Various approaches exist for this. Some claim that this isn't an issue at all, as the paranoia inherent in the game makes it challenging even if there is only one Cylon in the game. Other people disagree, and have devised various mechanics and house rules in order to deal with this situation, for example, here ("Avoiding 'Missing Cylon Syndrome'") or here (an execution variant for playing with Pegasus and Exodus). It mostly comes down to the balance in your specific game group with your play style.