Suppose some codons mapped to two different amino acids? what would the effect be on your translation of coded messages? what would the effect be on the production of proteins?

This will be detrimental on the production of protein. One amino acid can be coded by different codons but one codon cannot code for two different amino acid. The finished protein will not be the same every time, and since the amino acids have properties that determine protein structure and folding, then the function will not be congruent every time. 

For instance, if a hypothetical codon AAT codes for both glutamic acid and valine then a normal person will have both normal red blood cells and sickle cells since sickle cell disease is caused by the substitution of valine instead of glutamic acid on the position 6 of the beta subunit of hemoglobin. 

You should never redesign your experiment. try and see what in your experiment you made a mistake on or try and test your experimemt with somebody else. see if they get the right results.