Just guessing...
Check that you do not have the Mute button selected for an input channel in the Focusrite Mix Control app (whatever it's called for your interface).
Mix control only affects the mix that is sent to the output, and typically this would be used to create specific mixes for different outputs on the Focusrite interface, e.g., a monitor mix that's different for folks recording different parts. But, the default is the main outs. Put another way, muting in [Focusrite's] Mix Control app doesn't have anything to do with the mute button in Logic Pro X, i.e., the track still appears and gets recorded, you just don't hear it in the mix you are listening to.
It might help to attach screenshots of how you have your Logic Pro X project set up and the Mix Control app mix that's active.
Edit: attached my Saffire Mix Control app and Logic Pro X showing the muted channel (2) in a project. It records fine, but I cannot hear it in the output because that channel is muted in Mix Control. It is not muted in Logic Pro X.