Maybe the Doctor is just a bad pilot, or likes to pilot in eccentric ways:
[TARDIS shakes violently]
River Song: Use the stabilizers!
The Doctor: It hasn't got stabilizers!
River Song: They're the blue ones.
The Doctor: The blue ones don't do any thing, they're just blue!
River Song: Sure, they're blue - they're blue stabilizers!
[pulls blue levers, the shaking stops]
The Doctor: Oh, well now it's just boring, isn't it? They're boring-ers, that's what they are, blue boring-ers!
River Song: OK. I've mapped the probability vectors, done a foldback on the temporal isometry, charted the ship to its destination and... parked us right alongside!
The Doctor: Parked us? We haven't landed!
River Song: Of course we've landed - I just landed her!
The Doctor: But... it didn't make the noise.
River Song: What noise?
The Doctor: You know, the...
[imitates TARDIS noise]
River Song: It's not supposed to make that noise - *you* leave the brakes on!
The Doctor: Yeah, well, it's a brilliant noise. I love that noise.
Leaving the brakes on and not using the blue boringers could affect the course!