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Yoda: Always two there are, no more no less. A master and an apprentice.
Mace Windu: But which was destroyed, the master or the apprentice?

They were talking about the Sith.But the phrase can be used with Obi Wan and Qui Gon too.Cause Obi Wan defeated Maul(yes it was forced cause he's a key character in the saga), but he was able to do what is master can't.So maybe the two Jedi Masters were also talking about the death of Qui Gon, and of Obi Wan, cause the powers and the skills as the mind of the apprentice were probably growing over that of his master or on the same level.

i think your making the mistake of reading too much into star wars. although lucas has come up with a fairly complex storyline i really doubt he meant it to be picked apart for hidden meanings like it is.