Why have Soul and Maka got 0 souls in chapter 001a? In the intro chapter 000-1 of Soul Eater, it's stated that Maka has fed 99 human souls to Soul (the character), that's why they have gone after Blair (a seems-to-be witch) to collect the final soul for Soul (the character). 

In chapter 1 on page 20, they were forced to take extra lessons with Black☆Star because both of them didn't collect a single soul. Additionally, you can see Blair from the intro in the first few pages.

So my question is, why are Soul and Maka punished for not collecting a soul, when in the intro it's stated that they have collected all their 99 souls already?
There are quite certain conditions that need to be met in order for a weapon to become the Death Scythe. As looper mentioned in his answer, they need to collect exactly 99 souls + one witch soul. However, "human souls" is not a quite correct definition for those 99 souls. They are, of course, never encouraged to take innocent humans' souls, but rather 99 souls "that are on Shinigami-sama's list" (in manga), or 99 souls that are "on the way to becoming the Kishin" (in anime). So basically, those have to be "bad" souls. 

After that, just one soul of a witch is needed to complete the transformation. Usually the witch's soul is collected last, but if it's collected before the 99 other souls, it's kept within Shibusen until the 99 souls are gathered, and then gets taken out and consumed.

Now, if any other soul other than a witch's soul is eaten last, then all the souls that were eaten before it are lost, and the quests starts over again. In this case it doesn't matter at all that Blair


   was a cat, or anything else. The only thing that matters is that she was not a witch. 


That's why the 99 souls are reset.

Source: Death Scythe (Weapon)