Anyone have any ideas?

Did you touch out at Wembley Central? If you didn't then I can fully
understand why a touch in at Wembley Stadium would, in fact, end your
original journey from Picc Circus (as recorded on your card).

Something similar has happened to me before, about a year ago. Myself
and a friend got out at Canary Wharf and touched out. We then walked to
Westferry and tried to touch in again, and the LCD screen on the reader
said 'Exit' for both of us. No matter how many times we put our cards to
the reader the screen still kept saying 'Exit.'

We approached the Train Captain and he used his reader, both of our
cards showed the red light on his reader. He said it was odd but let us
travel. We were only going to Bank anyway so it wouldn't be a problem
for any future journeys.

At the end of the day we both checked out statements on the ticket
machines and for both of us it said said something like:
"Baker Street - Unfinished
Unstarted - Westferry"