Gosh darn. I just got a new Musical Fidelity A1 integrated amp, and I did the same thing, in the midst of my excitement over the new acquisition, that I did a few years ago with my newly-acquired vintage Marantz 2270. I connected a CD player to the phono inputs. DUH! DUH! DUH!
No clipping this time, but something else strange happened. When I set the amp to "CD" mode, I could faintly hear the input that was coming through the phono inputs. It sounded like the music was a mile away, but I could make it out barely. I tested the CD inputs and they sound fine, and now I'm waiting for a turntable to be delivered so as to test that function.
Hopefully there's no damage. I've wanted a high-quality audiophile amp like the A1 all my life, and this is my first, aside from the old Marantz! But why would I hear the input from the phono jacks when I had the amp set to CD mode? Does this mean that some boundary was crossed in the amp, and would it be damaged thereby? Maybe I need to go back to Fisher Price!