I would agree with the comments, normally it would just express surprise rather than 'I didn't want to see you here!' However, the way it is said carries a lot of meaning, if said in an angry way, with an annoyed tone of voice or in a shout, then it could also carry the meaning of 'Why are you here? I didn't want you to come!' Said in a pleasant way it would mean 'What a nice surprise, I'm glad to see you!'

It means I'm surprised to see you here.

its a surprise