There are a number of reasons you may not be able to check-in online. If you booked one segment as Frontier and one as Midwest, regardless of who operates the flight, you cannot check-in online. If that's not the case, the most likely situation is that your birth date information did not get passed to the Department of Homeland Security computers prior to check-in. That's a frequent occurrence and the check-in agent has to do it manually before the computer will issue a boarding pass.