"I didn't expect to see you here", does it imply I don't want to see you here or ?
"I didn't expect to see you here", does it imply I don't want to see you here or it is a surprise to see you here?

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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!'

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It means I'm surprised to see you here.

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its a surprise