Contradiction with Leviticus 19:18
This verse promotes love for one's neighbor and not holding grudges, which contrasts with the conditional plea for family sparing in Joshua 2:13.
Leviticus 19:18: Thou shalt not avenge, nor bear any grudge against the children of thy people, but thou shalt love thy neighbour as thyself: I [am] the LORD.
Contradiction with Exodus 20:13
This commandment against killing conflicts with the imminent destruction that Rahab seeks to avoid for her family in Joshua 2:13.
Exodus 20:13: Thou shalt not kill.
Contradiction with Matthew 5:44
Jesus' teaching to love enemies and pray for persecutors clashes with the selective sparing request seen in Joshua 2:13.
Matthew 5:44: But I say unto you, Love your enemies, bless them that curse you, do good to them that hate you, and pray for them which despitefully use you, and persecute you;
Contradiction with Proverbs 24:29
Advises against repaying others based on what they've done to you, contrasting with the quid-pro-quo agreement in Joshua 2:13.
Proverbs 24:29: Say not, I will do so to him as he hath done to me: I will render to the man according to his work.
Paradox #1
The contradiction in the verse might come from the fact that it involves a situation where lying and deception are used for a seemingly good outcome. This could be seen as conflicting with the general moral teaching against lying. Some might find it difficult to reconcile the use of deceit with adhering to moral principles.