There are two schools of thought on this matter.
The first is to simply accept that different instructors within the same system, will teach certain things in a different manner. In kata, this might simply mean a small change in a movement, or a radical departure. I may be a stickler for unity, but in the cases where the change is something slight, I'm pretty much willing to accept that it's a slight difference. This is, of course, assuming that the slight difference hasn't changed the meaning of the kata or its interpretation.
The second is to have every instructor refer to the absolute chief instructor of the style, and that everyone must do things his / her way, simply for the sake of unity. In an ideal situation, this system works exceptionally well, and there's no question about whose way is the right way, since everyone refers to the same source.
However, this world is far from ideal... We're all human beings, and sometimes, things diverge without us knowing that we're doing it. The second method also requires consistent communication between the style head and all of the other senior sensei of the style. I'm not saying that it can't be done (it actually has been done, and done quite well), but when a style of martial arts grows bigger and bigger, the number of divergences will also grow.
The reason why I generally favor the second method is based on what I've seen in the past. I'm not going to kid you here; sometimes, senior sensei within the style can argue in a heated manner, over who is right, and who is wrong.
The second method helps reduce internal strife within the system. Still, though, we're not all a bunch of robotic entities; different people will do things in subtly different ways, and to not be tolerant in the slightest of this isn't exactly productive.
Now for a bit of divergence myself!
This isn't just limited to kata, techniques, etc. In one extreme, I've seen a style go through a most ugly split, simply because of a disagreement as to who would be the next menkyo-kaiden after the soke passed away (even though he had willed it to one person). This rift still continues to this date, even though both factions have been quite successful. It's still an ugly thing, and something that unity amongst the senior sensei could have prevented.