check points while preparing for sequencing - (Sep/09/2011 )

I see now. You mean mismatches, where there are peaks of different nucleotides in a single position.
Now this can be caused by the things I mentioned above, but also it may be too high sequencing noise.

Do you sequence on ABI machine? Can you share the sequencing file? That would be even better than an image, it may be possible to check the raw data of the sequence.