LUKE: What was going on up here?
LUKE: Nothing? I walk in here and the two of you are like shrapnel.
Shrapnel, the common term for fragments of an artillery explosion (technically not quite correct, but good enough for our purposes). Luke means that Rory and Jess sprung apart when he came in like a bomb exploding in several directions at once.
Luke was so keen to see Jess and Rory together, but the minute he actually finds them just about to kiss, he freaks out. What did he think two eighteen-year-olds were going to do alone together?