Alternate genetic codes in newly sequenced organisms
If the organism uses an alternative code, the predicted protein sequences would always include the same type of amino acid substitution errors. This pattern should become apparent when you compare the proteins to other organisms.
In reality, the most common alternative code uses UGA for tryptophan instead of the usual stop. If you make the mistake of using the standard code for these genomes, the predicted genes would become highly fragmented so it is almost impossible not to notice.