Tesla, especially later in his life, was constantly monitored by the FBI. When he died, all his notes and other belongings were taken and, for a very long time, nothing was returned to his family. Has anything like this ever happened to another civilian scientist?
Andrew Weil, the mathematician was in Finland when WWII broke out and he was arrested on suspicions of spying; in fact, it was during his internment in Rouen he did the work he was most famous for and he wrote a letter to his wife saying:
My mathematics work is proceeding beyond my wildest hopes, and I am even a bit worried - if it's only in prison that I work so well, will I have to arrange to spend two or three months locked up every year? In the meantime, I am contemplating writing a report to the proper authorities, as follows: "To the Director of Scientific Research: Having recently been in a position to discover through personal experience the considerable advantages afforded to pure and disinterested research by a stay in the establishments of the Penitentiary System, I take the liberty of, etc. etc."
Lawvere became politically active during the Vietnam war and as he explains in an interview:
Some members of the team, including myself, became active against the Vietnam war and later against the War Measures Act proclaimed by Trudeau. That Act, similar in many ways to the Patriot Act 35 years later in the US, suspended civil liberties under the pretext of a terrorist danger. (The alleged danger at the time was a Quebec group later revealed to be infiltrated by the RCMP, the Canadian secret police.) Twelve communist bookstores in Quebec (unrelated to the terrorists) were burned down by police; several political activists from various groups across Canada were incarcerated in mental hospitals, etc. etc. I publicly opposed the consolidation of this fascist law, both in the university senate and in public demonstrations. The administration of the university declared me guilty of “disruption of academic activities”. Rumors began to be circulated, for example, that my categorical arrow diagrams were actually plans for attacking the administration building. My contract was not renewed.
There is a famous case of Luzin in the former Soviet Union when he was accused by the Soviet scientific establishment of being:
a paltry individual who pretends to champion “pure science” but betrays the interests of science, merchandizing it to appease you former bosses—the present-day masters of faschistoid science. The Soviet community will perceive the story about Academician Luzin as another object-lesson of the fact that the adversary never lays down his arms, that he camouflages himself more skilfully, that the methods of his mimicry becomes more diverse, and that vigilance remains the most demanded trait of every Bolshevik and every Soviet citizen.
I imagine that there were plenty of other cases.