See above for examples. The 3700 seems to have quite a tendancy to insert extra N's and even called nucleotides. Early in the run, when base spacing is a bit more variable, watch out for C-G dinucleotides with a bit of extra space between them. An N may get inserted there erroneously. As the gel progresses, it loses resolution.
Peaks broaden and shift, making it harder to call the bases accurately.
Watch for multiple bases of any one nucleotide where there really should be only one. Wide peaks later in the gel can be mis-counted by the program as two nucleotides. Wide peaks may also obscure smaller adjacent peaks. The 3700 can read as far out as 800 or 900 nucleotides, but in our hands so far, we only get such read lengths sporadically. Our two oldest machines get about 400 nt from good templates.