There are holes in every timeline theory; the only timeline that is actually flawless is this:
............/--WW/PH--ST
SS--OoT
............\MM--TP
Beyond that, there are going to be holes. In the above timeline, for instance, A Link to the Past being placed in the child timeline creates a hole - Ganon is ostensibly dead at the end of TP. Though a Ganon returns in Four Swords Adventures, there is some debate on whether that Ganon is the same Ganon (which he can't be, because he's dead) or a new Ganon (which many people say he isn't; either way, FSA being placed there creates problems). Even if we accept that FSA can be placed there, he is sealed in the Four Sword; in A Link to the Past, he is sealed within the Dark World, or Sacred Realm, and in possession of the full Triforce.
What this timeline does that others do not is provide a series of events that transpire between games on the timeline. While this is an exceedingly well-reasoned and very accurate timeline, it has holes like any other - holes that can only be resolved with Zelda games that cover certain events, like the Seal/Imprisoning War.