"你怎么来了?" How come you are here? "你怎么来的?" How did you come here? It's confusing in English too if you put it that way. :)

Thank you, Rose.

Thank you for your question, it helped me learn something new :)

“你怎么来了” means "Why are you coming here?" It contains the meaning that the speaker doesn't want him/her to show up. "你怎么来的" means "How did you come here?" It asks him/her the means of transportation he/she chose.