The rate of mis-called bases increases after the first few hundred nucleotides due to degradation of the sequencing gel. It is your responsibility to check for mis-called bases and to truncate the sequence when the error rate becomes too high. A small amount of baseline noise should not interfere with base calling. Peak heights may vary up to 5-fold. Resolution of the gel decreases towards the end of the run.
Peaks broaden and shift which makes it more difficult for the computer to call bases accurately.
Multiple bases of the same nucleotide may be mis-counted or broad peaks may be counted as multiple bases. When the data becomes too error prone truncate the sequence.