Jirachi must be fought in order to be recruited or grant wish. You must have Wish Stone to be granted a wish.
If you wanted to recruit it, read below. Otherwise disregard it I assume that you have space for Jirachi (team size <=5 and number of team members <=3). Do you have its Friend Area (Mt. Moonview)? Are you sure you didn't kill it from distance or Jirachi kills itself with a risk-taking move? Because that's probably the reason.