Continuity mistake: When Rita bails out of babysitting, she says, "Oh no, I have to work," pointing inward, but her finger is outward when she continues the phrase in the next shot. (01:56:20)
Continuity mistake: When Marcus and Mike drive towards the hospital they drive through a sandy beach and dust covers the car, but when they park the car is spotless.
Character mistake: The movie is set in 1999. Mike's ex was arrested on November 11, 1995. Mike then tells Marcus that he met her when he was an undercover cop in Mexico, fresh out of the academy, "twenty-four years ago," before he got partnered up with him. However, earlier in the movie, it's mentioned that Marcus has been married to Theresa for 26 years and partnered with Mike for 25 years.
Other mistake: Mike's undercover job ends in 1995 and has to take place before Marcus and him work together. The first "Bad Boys" takes place in the mid-nineties (there's a 1990 calendar but also a Michael Jordan retirement reference, so it's safe to say it's supposed to happen between 1993 and 1995). Mike mentions there that they have been partners at the precinct for six years. Moreover, in "Bad Boys 2," Marcus' yearbook from 1988 has Mike's signature with the Bad Boys motto; they were friends long before the first movie. There was no room for nerdy "Michael" to disappear for possibly years without Marcus knowing and the subject coming up before.
Plot hole: Isabel's escape can happen just because it's off-screen. For it to happen, it's critical that every single guard (minus the one she kills) is inside the monitors' room, but not a single one stays behind, because it needs that no guard can see what is happening, in person or remotely. No amount of other blindly loyal fellow prisoners who are staying behind can cover not only her fully switching her clothes, but also transporting the body (who was dressed up in full, even if there was no need for that) from the middle of the room to the nearest washing machine. It also needs the paramedics to completely bail out of doing their job; she is not Hannibal Lecter, she is not wearing the face of her victim, she has just some blood smeared on her and superficial cuts.