If you leave it at 0 ranks it will say it is N, which means native.
In karmagen, if i buy a knowledge skill, it has a value of 1 and i am not able to decrease it

I remember the situation you described there and it was definitely possible in Chummer in a previous edition, but not anymore sadly (at least not in karmagen).
Chummer assumes the MAG value set on the Attributes tab is the final Value you want, and 'increases' it (with Karma, iirc) when you spend essence.
As long as that is happening, this is working as intended. (If not, then therein lies the bug.
)
So, if i understand you right: If i have an adept with cyberware between 0,01 and 1 essence cost, i should buy MAG up to a rating of 5 and chummer will substract the karma it would need to pay for MAG 6?
In this case, Chummer is wrong. I just created an adept with a MAG rating of 5 and picked up cyberware with an essence cost of 0,2. I lost 10 karma points making this move. It should have been 30.
The same happens if you buy a MAG rating of 2 and buy the same cyberware. It costs you 10 karma points again, which cannot be right (should be 15).
Hope this will help!