The movie is the kind of movie that relies on the power of doubt, so it's not crystal clear for us to tell what happened.
But, based on a few reasons, we can assume that Lena is not a clone:
The lie fact
The lie fact, pointed out by @John
Clones do not have memories, or at least not much of it. When Kane gets out and returns to his home, he seems to not to be able to remember anything, not even Lena. The only reason he was there was that he somehow found Lena's face familiar.
Notice that memory loss occurred after he returned from the shimmering. In the ending, Lena can remember Kane, she asks where her husband is. The only reason Kane remembers Lena again is that they met AFTER Kane left the shimmering. So, giving that Lena remembers Kane, and cares about him, is a clue that she is not a clone.
Clones aren't afraid to tell the truth. It's pointed out by Dr.Ventress, and Lena herself, that they don't know what did the alien want, or if it wants anything at all. Kane also doesn't hesitate to answer any question, even when it puts him into danger by telling that he is not Kane. But when Lena doesn't answer, it can be a clue that she is not a clone but she is not sure.
Having a shimmering pupil doesn't necessarily mean that they are clones. Mutation is a side effect of the shimmering, so is growing leaves out of skin, but that doesn't mean you have to be a clone. Josie is affected by the same effects, but she is not a clone, and finally gives up her life, becoming a tree. Therefore you can't certainly say, shimmering pupils equal being an alien.