Isleworth Mona Lisa
According to Leonardo's early biographer Giorgio Vasari, Leonardo had started to paint "Mona Lisa" in 1503, but "left it unfinished". However, a fully finished painting of a "certain Florentine lady" surfaced again in 1517, shortly before Leonardo's death and in his private possession. The latter painting almost certainly is the one that now hangs in the Louvre. Based on this contradiction, supporters of the authenticity of the "Isleworth Mona Lisa" claim it is the unfinished "Mona Lisa", made at least partially by Leonardo, and the Louvre "Mona Lisa" a later version of it, made by Leonardo for his own use.
Isabella of Aragon, Duchess of Milan
In 2012, anthropologists excavated the body of Isabella, and concluded that she had syphilis. Her teeth had a high level of mercury, which was used (ineffectively) to treat syphilis, and had given a black color to the tooth enamel, most of which had been removed by abrading. They concluded that she was poisoned by her own medicine. 
Isabella was first suggested as the subject of da Vinci's "Mona Lisa" in 1979. This presupposes that the painting took place in the 1490s, during da Vinci's Milanese period. However, the painting has officially been dated as later, likely ruling Isabella out as the subject. Additionally, Isabella was never recognised during her lifetime as the subject of the painting. Those who viewed the "Mona Lisa" and were acquainted with Isabella such as Luigi d'Aragona and his secretary, Antonio de Beatis, did not make a connection.