The Trotters were bottom of the Championship heading into the encounter but were two goals up by the break, with Josh Murphy's strike for the visitors deep into stoppage time proving a mere consolation.
The result made it four straight losses in all competitions for the Canaries, who now go into the international break 13th in the Championship table.
"It is really frustrating. I am really annoyed we have lost this game. We couldn't see this coming," Farke told reporters. "We had everything under control at the start, we dominated the ball, created loads of chances and we were not effective enough.
"Bolton had two situations and scored two goals. It was pretty easy for us to defend these situations. We created some big chances and missed them until Josh Murphy scored late but it was too much. The problem is we are not able to be brutal or clinical in our finishing. We had the same problem in the last 11 or 12 games.
"In general, I think our defending behaviour is much better than the start of the season. It means we have to create more chances, we spoke about this and we did. Then it is about taking them otherwise if you are sloppy at the other end you get punished."
Next up for Farke's side is a home encounter with 16th-placed Barnsley when EFL action resumes on November 18.