"Excuse you" is usually said in sarcasm when someone does something rude and fails to apologize or excuse themselves. In the example you gave, Jake bumped into a woman accidentally and certainly should've apologized to her for it, but he didn't. Jess says "excuse you!" to let him know that not only did he bump her, but also that she found his behavior to be rude.
It's not considered polite when you do it to a stranger, but it's often said jokingly among friends and family members. For example, if your husband belches loudly you might say "excuse YOU!" in an exaggerated tone.
"Cracked" in the example you gave means Jess said it sarcastically.