CJam, 14 bytes
q~$W%2ew::#0&!
Test suite.
Explanation
q~ e# Read and evaluate input. $ e# Sort strings. If a prefix exists it will end up directly in front e# of thea string which contains it. W% e# Reverse list. 2ew e# Get all consecutive pairs of strings. ::# e# For each pair, find the first occurrence of the second string in the first. e# If a prefix exists that will result in a 0, otherwise in something non-zero. 0& e# Set intersection with 0, yielding [0] for falsy cases and [] for truthy ones. ! e# Logical NOT.