Dear Hanah,

A properly alignned codon file will often contain gaps, but they won't introduce premature stop codons. Please examine your alignment for gaps which happen in the middle of codons (e.g. runs of '-' which are not multiples of 3, as in A-GTCC--T). If you find many of them, then your alignment is most likely compromised by the alignment program which simply aligned nucleotides without regard for the coding structure. I would suggest translating your sequences to amino-acids, aligning the amino-acids with your favorite program (e.g. muscle or clustal), and then mapping those back to codons.

HTH,
Sergei