"Her dark brown hair and black eyes made her look mysterious. She had little freckles across her nose and she had olive skin which somehow made her look lighter. She had the cutest English accent but yet there was something about her that made me wonder what she was hiding".
The paragraph structure is just fine. I would suggest a few stylistic changes to the first two sentences:
"Her dark brown hair and black eyes gave her a mysterious look. Freckles across her nose somehow made her olive skin seem lighter. She had the cutest English accent, but there was something about her that made me wonder what she was hiding."
1) "made her" is too strong for what you're describing.
2) Same as #1, and to be more concise, and to avoid redundancy ("made her look" appears in both sentences).
3) The comma after "accent" is necessary, and the words "but" and "yet" are nearly synonymous and certainly redundant. Also, though I imagine this won't matter in the original context, the final period goes inside the end-quote mark.
The third/last sentence is worded nicely, and just needs a comma after "accent."
Adding to this, "yet" means up to this point. Everyone worked as quickly as they could yet we missed the deadline. There is no time element between the English accent and her elusiveness.. As far as the comma after accent goes; depends on the style. In journalistic style there wouldn't be a comma. It could probably go either way in prose but you should be consistent. Mediterraneans usually don't have freckles and I don't know how much this adds to the impact of the paragraph. Since you are the narrator I don't think you need to say "seems to me" who else would it seem to? I'd probably write: "Despite her cute English accent, her dark brown hair and black eyes made her seem mysterious; like there was something she was hiding."
True about the comma, but I assumed from the content that this was not journalistic writing. Where is there a "seems to me" in any of this??
The phrase I was thinking of was "made me wonder" I should have asked who else it would make wonder than the narrator?