Operating an engine includes injecting a first charge of liquid fuel using a first set of nozzle outlets in a fuel injector, and injecting a second charge of liquid fuel using a second set of nozzle outlets in a fuel injector. The first charge is autoignited in a first engine cycle, and the second charge is autoignited in a second engine cycle, and may be used to pilot ignite a charge of gaseous fuel. Operating the engine further includes limiting errors in targeting of the second charge of liquid fuel caused by transitioning the engine from a first combination to a second combination of speed, load, and boost, by varying an injection pressure of the liquid fuel from the first engine cycle to the second engine cycle.