Transitioning from a BS in CIS to an MSE in Software Engineering
Most MSE programs in the US do not require you to have a BSE in the relevant field. The listed prerequisites for the courses are often requirements that undergraduates need to fulfil before being allowed to enrol in the graduate class. That said, you may need to take some undergraduate classes to get up to speed and you may need to work harder to make up for starting slightly behind. If accepted, it is likely that the admissions committee thinks that your previous background is enough to be able to succeed in the program.

In summary, admissions committees do not accept students that they think will be unable to complete the program.