Why was Matthew Flinders imprisoned?

Answer 1

After circumnavigating Australia, Flinders was returning to England when he was shipwrecked, in 1803. He sheltered with his crew (and his cat Trim) for two months in tents on islands. When some ships finally came to rescue Flinders, he chose to go aboard the small schooner Minikin rather than go aboard a larger, sturdier ship. The Minikin started to leak and Flinders was forced to take shelter on a French island, where he was taken for a spy. At that stage, Flinders was unaware that England and France were at war, and despite his protestations of innocence, the French insisted on detaining Flinders. The French kept Flinders prisoner for almost seven years.

Answer 2

He violated the terms of his scientific passport by changing ships and carrying prohibited papers.