Contradiction with Genesis 1:1
Ephesians 3:9 mentions God who created all things by Jesus Christ, while Genesis 1:1 states God as the sole creator without mention of Jesus Christ.
Genesis 1:1: In the beginning God created the heaven and the earth.
Contradiction with Isaiah 44:24
Ephesians 3:9 talks about creation through Jesus Christ, whereas Isaiah 44:24 emphasizes that Jehovah alone created the heavens and the earth.
Isaiah 44:24: Thus saith the LORD, thy redeemer, and he that formed thee from the womb, I [am] the LORD that maketh all [things]; that stretcheth forth the heavens alone; that spreadeth abroad the earth by myself;
Contradiction with John 1:3
While Ephesians 3:9 distinguishes God creating through Jesus, John 1:3 attributes all of creation directly to the Word, identified as Jesus, with no intermediary.
John 1:3: All things were made by him; and without him was not any thing made that was made.
Contradiction with Colossians 1:16
Ephesians 3:9 implies God used Jesus as a means in creation whereas Colossians 1:16 states that all things were created by and for Jesus without an intermediary role.
Colossians 1:16: For by him were all things created, that are in heaven, and that are in earth, visible and invisible, whether [they be] thrones, or dominions, or principalities, or powers: all things were created by him, and for him:
Contradiction with Hebrews 1:2
Ephesians 3:9 suggests a collaborative act in creation between God and Jesus, while Hebrews 1:2 specifies that God made the worlds by His Son, indicating a direct action.
Hebrews 1:2: Hath in these last days spoken unto us by [his] Son, whom he hath appointed heir of all things, by whom also he made the worlds;
Paradox #1
The idea in Ephesians 3:9 that God created everything can conflict with scientific explanations like the Big Bang theory, which suggests a naturalistic origin of the universe. This difference lies in whether you view the universe's beginning as a divine act or a natural process.