Anatomically they are all there, in the sense that the components are present and connected correctly; the knees are very good. The legs have been drawn as if with a thicker layer of subcutaneous fat than a typical male, allowing the artist to avoid dealing with difficult detail in thigh and calf. Proportions and forms are OK, with the exception of his almost tubular left quadriceps, which flares towards the knee rather than tapering.
The main reason the legs look strange is the artist's use of light and shade: Mars's right thigh is lit from below, but his right calf and left leg are lit from above; this inconsistency puzzles the eye. Also, his right calf casts no shadow onto his left leg, which makes the legs look oddly crossed. Finally, the line running along the bottom of his left leg, separating it from the pink robe/blanket, seems to cut through the flesh, making it hard to understand the shape of the posterior musculature.
I think it is fair to say that Botticelli had the knowledge and skill to do 'better', he simply didn't choose to: he was a breaker rather than a maker of rules, and you can either take his work or leave it.