How do Catholics defend the apparent errors found in the deuterocanonical books?

"Condones the use of magic"

Tobit is the subject of an extensive commentary by Venerable Bede, who is accepted as a Church Father by both east and west. He explains that Tobit is to be understood in an allegorical sense and not a literal/historical sense. Regarding things like smoke from a burnt entrails driving away evil spirits being "superstitious" and having "no place in the word of God", we might likewise expurgate the account of Jesus healing a blind man by spitting on dirt from the Gospels (John 9:6). In Tobit, the passage regarding the fish entrails is not given as general advice, as one might find in Proverbs, but is specific direction given to Tobit by an angel for occasions specific to him. There are many other examples in the Old Testament and New of men directed to use created matter for spiritual purposes.

"Salvation by works"

The two verses cited state that alms deliver one from sin and death. They do not say that alms bring about forgiveness of sin. One might consult here:¹

Proverbs 10:2

Treasures of wickedness profit nothing: But righteousness delivereth from death.

The author of the article emphasizes 1 John 1:7 here (the blood of Jesus His Son cleanses us from all sin), but fails to acknowledge the parable of the sheep and the goats (Matthew 25:36-41) and completely ignores Revelation 20:12:

And the dead were judged out of those things which were written in the books, according to their works.

"Money as an offering for the sins of the dead"

The author attacks 2 Maccabees 12:43:

And when he had made a gathering throughout the company to the sum of two thousand drachms of silver, he sent it to Jerusalem to offer a sin offering, doing therein very well and honestly, in that he was mindful of the resurrection

The author comments:

Can anyone truly accept that money isn't offering for the sins of dead people? Such a superstitious and unbiblical concept has no place in Scripture.

The concept can be considered as "having no place in Scripture" and "unbiblical" only if one chooses to exclude 2 Maccabees itself from Scripture. This is a non sequitur. 2 Maccabees was designated for inclusion in the Old Testament canon in the 85th Apostolic Canon as well as by the Council of Carthage of 397 in the west (Canon XXXIII), later ratified in the east as well.

Augustine wrote an entire commentary on the passage attacked by the author as follows, with an acknowledgement that the teaching is unique. His introduction reads:

In the books of the Maccabees we read of sacrifice offered for the dead. Howbeit, even if it were no where at all read in the Old Scriptures, not small is the authority, which in this usage is clear, of the whole Church, namely, that in the prayers of the priest which are offered to the Lord God at His altar, the commendation of the dead hath also its place. But then, whether there be some profit accruing unto the soul of the dead from the place of its body, requires a more careful inquiry. And first, whether it make any difference in causing or increasing of misery after this life to the spirits of men if their bodies be not buried, this must be looked into, not in the light of opinion however commonly received, but rather of the holy writ of our religion.²

The balance of the essay can be found here.

"Historical Errors"

The author cites "wrong historical facts" in three verses within the books of Judith and Baruch. Eliminating these books on this basis alone would probably also lead to the elimination of:

• The Gospel of Luke, which maintains that Arpachshad was the grandfather of Shelah (3:35-36), since Genesis teaches that Arpachsad was the father of Shelah

• The Book of Numbers, which states that the Nephilim survived the flood (13:33), contrary to Genesis 7:21

• 1 Chronicles, which incorrectly lists Timna and Amalek as sons of Eliphaz, contradicting Genesis 36:11ff.

• The Book of Revelation, which leaves out the tribe of Dan (7:4-8)

• etc.

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¹ All of the Bible quotes - including 2 Maccabees 12:43 - are taken from the King James Version (which originally included the deuterocanonical books, or "Apocrypha")
²On Care to Be Had for the Dead