Contradiction with Exodus 39:1
This verse discusses the making of garments for the priests, which differs in content from the detailed description of onyx stones and engraving in Exodus 39:6.
Exodus 39:1: And of the blue, and purple, and scarlet, they made cloths of service, to do service in the holy [place], and made the holy garments for Aaron; as the LORD commanded Moses.
Contradiction with Exodus 39:32
This verse talks about the completion of the tabernacle work, which contrasts with the specific task of making the onyx stones specified in Exodus 39:6.
Exodus 39:32: Thus was all the work of the tabernacle of the tent of the congregation finished: and the children of Israel did according to all that the LORD commanded Moses, so did they.
Contradiction with Exodus 28:9
This verse also commands the use of onyx stones for engraving the names of the sons of Israel, but unlike Exodus 39:6, it serves as the initial instruction rather than the fulfillment of the task.
Exodus 28:9: And thou shalt take two onyx stones, and grave on them the names of the children of Israel: