The answer to this question can be found in Chapter Twenty Five of this excellent coming-of-age novel. Having left Phoebe a note telling her that he is going to head out and to meet him at the museum so that he can return the Christmas money that he took from her, Holden then waits for her. However, Phoebe arrives late, and it is clear from her description when she arrives why she arrived late and what precisely caused the delay:
The thing I couldn't understand, she had this big suitcase with her. She was just coming across Fifth Avenue, and she was dragging this goddam big suitcase with her. She could hardly drag it.
Thus we can see that Phoebe is late because she was busy packing this suitcase and then she was delayed in meeting her brother at the museum because of the weight of the suitcase and the way that it impeded her progress. Of course, as we read the rest of the chapter we realise that Phoebe packed the suitcase because she wants to leave with Holden as well.
While there is a specific reason to as why Phoebe is late (she is packing a suitcase so that she may leave with Holden), there could be a hidden meaning to her lateness as well. Perhaps, in my interpretation, Phoebe represents all that Holden is running away from- his own personal obligations. Every other time that Holden wishes to talk to someone or meet someone, Holden does not feel like it or he is excruciatingly early. It is here, the meeting at the museum, in which Holden no longer controls the time movement of the novel; Phoebe does. Therefore, one could interpret this as the one time where Holden does not control what is happening to him. Instead, Phoebe has such control over Holden that he begins to fear that he has lost control over his own life.