And we say "appeared" because it literally appeared there during the edit between those two scenes. The tyrannosaur breaks through the fence, then the heroes crawl through the broken fence the dinosaur just burst through, only to find the concrete wall you see above. How in the hell did the dinosaur scale that? With its tiny little T. rex arms? Hell, the only reason hiding down there works is because the T. rex can't chase after them. Is it like when a little kid climbs up a tree and then is too scared to get back down?
We'd say it flew up there, or jumped, but we actually see it standing on the other side of the fence -- on the ground that, one minute later, we see doesn't actually exist:
Seriously, is it up in a tree?
It's a testament to Spielberg's filmmaking wizardry that the vast majority of people never notice that one of the most famous scenes in his career has the spatial continuity of a Tommy Wiseau film. Unless, of course, you decide that it's not a plot hole at all, and just assume that hidden in the cuts of this sequence is the fact that Isla Nublar just underwent the biggest, most stealthy geological shift in history: Not only did the island swallow an entire jungle, but it covered up its crime with cement.
This revelation changes everything. The tension of our weak human characters facing off against a species that is stronger, faster, and bigger than them is somewhat tempered by the fact that they have a freaking sentient island on their side. It also explains all the other plot holes: Where'd the T. rex come from in that big hero scene? The island threw her there. Why did Dennis Nedry get so lost? The island hates fat people.
"Goodbye, Nnnnnnnewman." -Isla Nublar
Which, incidentally, proves our theory we just made up: Jurassic Park takes place on the same island as Lost. Now go, fan fiction writers ... go change the world.