Definition from Wiktionary, the free dictionary
See also bubo
- Possibly from bug-a-boo, an imaginary evil goblin.
- Possibly from bubo, a swollen lymph node especially obvious in sufferers of bubonic plague.
- Possibly from the sound a baby or young toddler might make.
Alternative forms 
boo-boo (plural boo-boos)
- (colloquial, often childish) A mistake or error.
- (colloquial, childish, by or to young children) A minor injury, such as a cut or a bruise.
- (error): blooper, blunder, faux pas, fluff, gaffe, lapse, slip, stumble, thinko
- (minor injury): owie, scrape, bruise, nick, scratch
Usage notes 
Sometimes used sarcastically when the speaker believes the listener is overreacting to a very minor injury, as in Aw, did the little boy get a boo-boo?