If I understand you correctly, you have removed the nut that holds the clutch inner hub on, the hub will start to slide off, but then hangs up on the end of the transmission input shaft?
If this is correct, then yes, look at the end of the input shaft an see if there are any rags or damage. If so, carefully file down the damage until the hub is able to come off freely.
However, it sounds odd. Are you sure you have disconnected everything? Is the inner hub hanging up on the outer basket?