"Despite the fact" implies knowledge of said facts

The headline does not state whether the officials knew of the girl's citizenship, but this can't be attributed to the choice of despite the fact that. The information about their knowledge would be clear if the headline read:

US Immigration officials deport 14 year-old runaway to Colombia, despite the fact that they know she's American and speaks no Spanish.

I'd say the headline lacks information, I wouldn't necessarily call it misleading.

Sure, I'll take the other side. The structure of the headline is: agent does X, despite Y. To me this means precisely that the agent acts in disregard of Y. It is meaningless to speak of disregarding something you are not aware of. So the corollary is that that the agent is aware of Y.

The headline means:

US Immigration officials deport 14 year old runaway to Colombia, disregarding the fact that she's American and speaks no Spanish.

So, presuming the article goes on to report that officials did not know the runaway was American, the headline is misleading.

I don't think it is misleading at all.

The headline is intended for the reader's benefit. The fact is -- or will become -- clear (to the reader) that she's American and speaks no Spanish.

In no way does the headline imply that the officials knew that fact... or even if it was a fact at all at the time... These are questions which the reader may have and, hopefully, which the reader will learn from reading the article.

It looks like you're getting tripped up by "the fact that". This appears to be a grammatical construct to overcome English's inability to apply prepositions to the conjunction "that". To solve the problem, we put in a dummy noun phrase, to which the "that" is applied. So, instead of saying "despite that she speaks English", we say "despite the fact that she speaks English".