There is some speculation that, on some level, Martha still loves the Doctor. When you see someone you love, your irises contract (or your pupils dilate, same thing). The Doctor noticed that evil clone Martha's eyes did not change on seeing him and deduced that it was a clone (as she had no physical response to him because she had no feelings for him).
On the other hand, he totally failed to spot our Martha's engagement ring even when it was there right in front of him at the start of TSS when Martha brushed her hair back off her face.
There is some speculation that, on some level, Martha still loves the Doctor. When you see someone you love, your irises contract (or your pupils dilate, same thing). The Doctor noticed that evil clone Martha's eyes did not change on seeing him and deduced that it was a clone (as she had no physical response to him because she had no feelings for him).
On the other hand, he totally failed to spot our Martha's engagement ring even when it was there right in front of him at the start of TSS when Martha brushed her hair back off her face.