Doing an amended tax return for my niece because her boyfriend entered all her amounts from her w-2 incorrectly. now it says she owes, why?

To see whether your amendment Form 1040-X is correct, you must visually compare the original and the correct Form 1040.

OR
blindly go with whatever TurboTax produces (not recommended).

since her boyfriend seems to have over-reported her income and under-reported her withholding, it is likely she would have ended up owing on the original return.  if that payment was made you need to take credit for it on the amended return - line 16.

the other possibility is that with multiple w-2's not enough was withheld.    for example the withholding on 3 - $15,000 w-'2's is going to be significantly less than the income tax liability on the $45,000 in total income