Lapsus meus gratiosus
A lapsus (noun, masc.) is literally a slip, a fall, extended to mean a mistake, including a moral mistake. These senses live in English "relapse", "collapse", and of course "lapse". It appears in phrases such as lapsus linguæ, "a slip of the tongue". Christianity uses lapsus to refer to the fall of Adam, whence some unusual English words like "prelapsarian" and "postlapsarian". A lapsus carnalis or lapsus carnis is a "sin of the flesh".
Meus means "my". I put it here after the noun in order not to give it strong emphasis. Putting a possessive pronoun before the noun tends to make it the main point: meus lapsus would mean "my mistake", putting most of the emphasis on the father.
Gratiosus (adjective) is filled with 2,700 years of accumulated positive connotations. Gratus primarily means beloved, dear, pleasing, commonly extended to mean worthy of thanks—a sense that lives in English "gratitude". There is also the well-known Latin phrase persona non grata, a person who is not welcome; so, a person who is grata is welcome, i.e. gladly admitted into the community. As a noun, gratia, it means favor, both that felt by others and favor felt toward another. Christianity picked it up as "grace", and it occurs in such established Latin phrases as Dei gratia regina, "Queen by the grace of God", still used on coins in Commonwealth countries. The suffix -osus is like Anglo-Saxon -ful in English: it makes an adjective signifying an intensified version of the noun. Gratiosus primarily means enjoying the favor of others: popular, beloved—especially, due to agreeable qualities about oneself. In other words, a person who is gratiosus is one that others are very glad to have around. This is imported into English as "gracious", a word which your friend appears to have chosen quite propitiously.
So, I'm thinking that combining the connotations of lapsus with those of gratiosus creates the same benevolent irony of "my gracious mistake". Maybe it's even clearer in Latin!
If the father wants to address the son by this phrase, he should use the vocative case, which comes out:
Mi lapse gratiose
(Note that the e's are both pronounced, like e as in Spanish.)