Are you saying you are trying to scan a paper boarding pass's bar or QR code with the PassBook "Scan Code" function? That will not work.
The "Scan Code" function is looking for a URL encoded into a QR, Aztec or PDF-417 code that will take it to a downloadable pass. For example, the following QR code will give you the sample, PassKit.com demo pass I posted yesterday. Scan this with the Passbook "Scan Code" function:
Image
(When you're done, click the (i) icon on the lower right of the pass and then the "Delete" button on the top left)
FYI, OT but if you use a generic Bar Code scanning app like Manatee Works, "Barcode Scanners" and point it at your boarding pass, you'll see the TSA mandated itinerary data is all in it. My latest one has stuff like this:
Code:
M1SMALLING/ERIC ABCDEF DFWPHXAA 1083
...
You can see my name, record locator (I changed it ABCDEF), city pair, carrier, flight number, and it goes on and on plus has some codes (probably a digital signature or something). When PassBook saw something like that it knew wasn't a URL to a Pass so it immediately gave up.