How did Batman end up in Alfred's car

Alfred is an ex-military man who acquired a number of advanced and practical skills. Considering his capability with mechanics and engineering, it stands for reason that he is able to locate and retrieve wounded individuals.

However... this scene is glossed over in the movie for theatrical purposes.

There's no help in the script or the novelisation. I assume the missing scene (where Alfred parks the car, heads up to the roof, spends some time looking for Bruce, then helps him down to the car) was ignored because it's trivial and doesn't advance the plot.

In the screenplay he simply calls Alfred and in the next scene he's in the car.

Batman smashes through the window, cloak ablaze … Falling … Tries to activate his cloak – but only gets one side to pop open … the deployed wing causes him to spiral.
Insert cut: Young Bruce falling, falling in the well shaft –
Batman plummets, trailing flame, unopened wing fluttering with the violent flapping of –
Bats: screeching, flapping, fluttering darkness …
Batman’s stiff wing hooks a railing – slows him with a jolt – rips – dropping him to the ground with a crash …
Young Bruce hits the dirt at the bottom of the shaft –
– and a sizzle, as wet pavement damps the flames. Groaning, Batman rolls his burning Batsuit along the asphalt.
Two Men at a hole-in-the-wall store stare at Batman, astonished.
Batman, smoldering, looks up: the two Men loom, menacing. Batman lurches into an alley … the two Men look at each other, dumbfounded. Batman raises his grapnel-gun, fires up at the enclosed roof – rides up – punches his way through wire and metal, crawls onto his back, staring up at the skyscrapers of Gotham. Rain blurring his vision.
Insert cut: Young Bruce watches his father crumple.
Batman fumbles at his belt. Pulls out a tiny phone.
BATMAN: (hoarse) Alfred?! Alfred?!

INT. ROLLS – LATER 148

Alfred drives, looks through the rear-view mirror at Batman, who lies in the back, flinching at invisible antagonists.

Interestingly, in the novel he doesn't use his grapnel gun at all, he just lies in the alley waiting for Alfred to arrive which actually makes more sense (but is less cool):

Batman stepped into the light of a streetlamp—a gaunt, black figure with smoke rising from it.
“Never mind,” the man said, and he and his companion ran.
Batman limped into an alley and from his utility belt pulled out a tiny phone. He pressed a button, and in a hoarse whisper said, “Alfred?”
Forty minutes later, Batman lay sprawled on the rear seat of Alfred’s Bentley as Alfred turned toward the manor. The smell of scorched fabric filled the car.

Purely as a matter of interest, in many prior versions, both Batman and Robin's belts contains a tracker device that allows Alfred to locate them in emergencies.