Freak can mean a few things weird and crazy are the most common. Sometimes these are used as a complement.
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It could mean that he finds you unique or different in a positive way, or it could be meant as a playful or teasing comment. However, context and tone are important in understanding the true intent behind the statement. If it makes you uncomfortable, it's important to communicate that to the person.
Unless he apsautally hates, you it probably means he is just trying to make convocation with you. Remember boys express there feeling in strange ways so don't be fooled.