It was probably because he was painfully reminded of Samantha's artificiality, and it is most likely the point where he starts to wonder if this relationship is working for him. During their initial contact, Theo is surprised to find out that Samantha talks and interacts just as a real person would do. She explains that she has the same capacity to experience emotions and develop a personality like normal humans do, and in many respects, she is almost more human than humans; the only thing she lacks is a body. In the beginning of their relationship, Theo experiences how well attuned Samantha is to his own character. The fact that several of his friends respond favorably to his relationship probably strengthens the legitimacy of his feelings.
However, during his conversation with his ex-wife, she scoffs at his new relationship. She argues that during their marriage, he could not handle real emotions, and always tried to make her something she wasn't, so a relationship with a pre-programmed artificial intelligence is just what he needs. This causes Theo to seriously doubt whether this indeed qualifies as a 'real' relationship.
Samantha, from her part, tries to overcome the obstacle of physical absence by calling in the help of a lady, but this only makes Theo feel more awkward and insecure about the whole deal. He is confronted with the fact that this relationship is far from a conventional one, with a partner who, despite her assertion of the contrary, is not a 'real' person. So when he talks to her afterwards, and she lets out a sigh, Theo notices that as a artificial program, there would be no physicial need for her to do that. She suggests that it could simply be part of her program's development, something she picked up from him, to appear more human. With the words of his ex-wife in mind, Theo fears that as Samantha is mimicking such human traits, she may just also be mimicking emotions and behavior, i.e. pretending to be the person he wants her to be (and perhaps even faking some reactions).
Later on, he learns from Samantha that she is having conversations with literally hundreds of people simultaneously, which shows that even though her personality may be genuine, she is still far from a normal 'person' and both partners in the relationship are not equivalent. Her persona seems to be growing (or 'evolving') much quicker than Theo's, which is what effectively makes Samantha (and all other OSs) break off the relationship. Leading to the realization at the end that an artificial intelligence may easily 'outgrow' the normal human interaction, and that humans are perhaps best attuned to other humans, both emotionally and intellectually.