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Recently a discovery was made of a ~12,000 year old girl in Hoyo Negro in Mexico.

This has been covered by many different news agencies.

I'm confused however by many of the reports. Does it strengthen the hypothesis that the ancestors to the Native Americans came over the Bering Strait? Or is there still some doubt on the matter?

Additionally, what are the arguments against the Bering Strait migration?

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As far as I can remember from skimming the published paper, it does provide support to the hypothesis that the first Americans probably migrated over a Bering Strait land bridge sometime during the last ice age. Remember, individual scientific findings rarely "prove" anything, they just support or refute a certain hypothesis (what a layman would call a "theory", a word which has a rather different meaning when used by scientists). –  MattDMo May 29 at 20:38
    
I would rather call it hypothesis for this reason instead of theory. –  Chris May 29 at 21:05
    
@MattDMo, updated to reflect your and Chris' suggestions. –  paqogomez May 29 at 21:16

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The discovery strengthens the bering strait land bridge hypothesis because if I remember right they did genetic analysis and her ancestors were almost certainly east asian. As for opposing migration models, they involve boats. Some evidence exists for polynesians reaching the west coast of south america, but probably in small numbers and not before humans walked in from the north. There is more information here: https://en.wikipedia.org/wiki/Models_of_migration_to_the_New_World

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