-ないと

[mella]

In a manga I am reading this sentence
気を付けないと
has been translated as affirmative, even if -ない is negative. Is -ないと a special grammar structure that I haven't yet studied?

[blutorange]

How was it translated? Literally it means "if [you] don't pay attention, then...". More naturally, one could turn this into an affirmative by saying "[you] need to / should pay attention". Please see http://www.guidetojapanese.org/conditional.html#part2

Also, note that there is a big difference between "literal translation" and "natural translation": Especially for languages quite a bit different from English such as Japanese, it often happens that although the literal meaning contains a certain grammatical structure &c (eg negative), the best way to say it in English may not contain that certain grammatical structure (eg using a positive+should).

For example, instead of
I am not eating food.
which uses a negative, I could as well say
I am currently doing something else other than eating food.
which uses an affirmative construction, yet the meaning is almost the same.

[squarezebra]

To put it another way, is a contraction, or an incomplete sentence. The full sentence would have (probably) been 気を付けないといけない (which is a double-negative) which means you MUST pay attention (for whatever reason). In casual spoken Japanese, parts of speech are often dropped and you just have to get used to this through exposure.