The TARDIS is unreliable.
We know that the Doctor has always had trouble getting the TARDIS to do exactly what he wants. The justification is sometimes that she's old and banged-up, sometimes that she's willful, and sometimes that he's just a bad driver, but the consistent effect is that relying on the TARDIS to get you exactly where and when you want to go is a gamble under the best of circumstances (which Angels Take Manhattan certainly wasn't).
Although the Tenth Doctor blamed his bad driving on needing more people to properly fly the TARDIS, and "Sexy" claimed the TARDIS took him where he needed to be, rather than where he wanted to be, these are both very flimsy:
- The idea that a TARDIS needs multiple pilots is downright laughable --as is River Song's claim that the VWORP noise is due to leaving the brakes on-- since both the Master and the Rani flew different TARDISes with only a single pilot without any of the reliability problems the Doctor experiences, but with the VWORP.
- Sexy's claim is the more supportable, but it doesn't justify the many times that the TARDIS's unreliability has been a major hinderance to the Doctor being where he truly needed to be. It's useful to remember that the entire first season story arc of Doctor Who was based on the idea that he had no clue where or when the craft would go when he used it.
The TARDIS is especially unreliable over short distances. Sometimes.
This varies depending on production team and the needs of the plot, but the TARDIS is frequently depicted as being bad at short hops. She's designed to run through all of space and time, so moving a couple miles in the same time frame is rather like using a backhoe to organize your silverware. The Doctor has mentioned this repeatedly since the 60s (Second Doctor era at least), and while he sometimes says that he's getting better at short hops, it usually regresses again quickly.
This is one reason the TARDIS can also move like a more normal flying object: it's easier to pinpoint your destination that way. The TARDIS flew through physical space in normal time at the opening of the 1968 story Fury From the Deep, and several times later in Old Who (including at least part of the crash which caused Six's regeneration into Seven).
A common analogy is the Enterprise, which has warp drives for her primary movement option but also has regular thrust engines to make small adjustments. However, the TARDIS's "normal" movement option is very... attention-grabbing... and the Doctor doesn't seem to be a very good driver in that situation either (he bangs about quite a bit and causes un-Doctorly collateral damage).