I think you probably hit the nail on the head with "He looked like he'd had a long duty day.."
It is obviously desirable to always present a tidy appearance however on the grounds of been there, done that, and got the (grubby) tee shirt, It doesn't always happen.
Being human, the pilots often need to answer the call of nature in flight, and sometimes just need to stretch their legs. It often happens that using headsets all day, hair does get messy. Clothing gets crumpled and stained with biro's and window grease and meal trays and spilt coffee etc.
On short flights (eg shuttles) it may be necessary to leave the flight deck even though the aircraft is manouvering. This is not desirable but it sometimes happens.
As any Pilot will tell you, manageing an aircraft can sometimes be a tireing, hot, grimey, busy, frustrating business. We would always like to present a tidy appearance but it doesn't always happen. If this is all you had to worry about on your flight then I don't think you have too much of a complaint.