The newly established nitrifying bacteria (nitrobacters) that have developed are just babies, and they need time to mature and multiply. These bacteria are living entities that to survive require oxygen, and food (ammonia or the bio-load, which is primarily generated by waste from all things living in an aquarium). Living on the surfaces of everything in the system, the larger their numbers, the better they are able to absorb the bio-load placed on the aquarium. However, when the bio-load "exceeds" the nitrifying bacteria population established, ammonia will begin to show up in the aquarium again, and if the load is extremely heavy the reappearance of nitrite is most likely as well.
To better understand how aquariums react to various types of bio-loads placed on them, view our Bacteria Population VS Bio-Load Ratio Reactions Table.
Once your tank has completed its cycle, if you move too quickly in adding new livestock or overly disturbing your biological filter, you may experience a case of New Tank Syndrome, so proceed slowly at this point.