I don't find the films inconsistent at all.

First, the films never directly indicate that Obi-Wan was Yoda's padwan. What we do know is that Yoda was 'the Jedi Master that once instructed me' and that Obi-Wan was an impatient student ('Was I any different?').

However, I think the answer is that Qui-Gon was killed before Obi-Wan could complete the trials to become a Jedi, and Yoda became his surrogate Jedi instructor preparing him for the Jedi trials.

Furthermore, because Obi-Wan sat on the Jedi Counsel, we can conclude he achieved the title of 'Master'. Perhaps Yoda was the one whom continued his training on the way to the title of Master.

This seems like a very reasonable way to explain it, and it does nothing to harm continuity.