I assume that you're using the NetFx45Web package from the NetFxExtension, which means you're using WiX's built in way of detecting it.
I'm guessing that by application, you mean your managed BA. You have to make sure you setup your BootstrapperCore.config properly. If your MBA needs 4.5 or later, then make sure the supportedRuntime element has 4.5 and not 4, same with the supportedFramework element.