why am I getting 'ugly' output?

At this point you should consider creating a small GUI for your input selection. But for your question at hand: you forgot to allign the start of the rows, so you missed the fact that they were actually shifted. The smart allign button in the editor and a few spaces gets you this:

combinations_available=input(['Enter the number associated with the combination of salts available. Enter 0 if none of the combinations are available.'...
    '\n1:Two of these chlorides        1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl(sodium chloride)   5) KCl(potassium chloride) '...
    '\n2:ZnBr2(zinc bromide)        &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride   4) NaCl(sodium chloride)   5) KCl(potassium chloride)'...
    '\n3:NH4Cl(ammonium chloride)   &  1) CH3CO2K(potassium acetat)   2) ZnSO4(zink sulphate)       3) HCOONa(Sodium formate)   4) HCOOK(potassium formate)'...
    '\n4:ZnBr2(zinc bromide)        &  1) CH3CO2K(potassium acetate)  2) ZnSO4(zink sulphate)       3) HCOONa(sodium formate)   4) HCOOK(potassium formate)'...
    '\n5:CH3CO2K(potassium acetate) &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl(sodium chloride)  5) KCl(potassium chloride)'...
    '\n6:CH3CO2K(potassium acetate) &  1) ZnSO4(zinc sulphate)        2) HCOONa(sodium formate)     3) HCOOK(potassium formate)'...
    '\n7:ZnSO4(zinc sulphate)       &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl(sodium chloride)  5) KCl(potassium chloride)'...
    '\n8:ZnSO4(zinc sulphate)       &  1) HCOONa(sodium formate)      2) HCOOK(potassium formate)'...
    '\n9:HCOONa(sodium formate)     &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl(sodium chloride)  5) KCl,(potassium chloride)'...
    '\n10:HCOOK(potassium formate)  &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl                   5) KCl'...
    '\n11:HCOONa                    &  1) HCOOK. ']);

With the result in the command prompt:

Enter the number associated with the combination of salts available. Enter 0 if none of the combinations are available.
1:Two of these chlorides        1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl(sodium chloride)   5) KCl(potassium chloride) 
2:ZnBr2(zinc bromide)        &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride   4) NaCl(sodium chloride)   5) KCl(potassium chloride)
3:NH4Cl(ammonium chloride)   &  1) CH3CO2K(potassium acetat)   2) ZnSO4(zink sulphate)       3) HCOONa(Sodium formate)   4) HCOOK(potassium formate)
4:ZnBr2(zinc bromide)        &  1) CH3CO2K(potassium acetate)  2) ZnSO4(zink sulphate)       3) HCOONa(sodium formate)   4) HCOOK(potassium formate)
5:CH3CO2K(potassium acetate) &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl(sodium chloride)  5) KCl(potassium chloride)
6:CH3CO2K(potassium acetate) &  1) ZnSO4(zinc sulphate)        2) HCOONa(sodium formate)     3) HCOOK(potassium formate)
7:ZnSO4(zinc sulphate)       &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl(sodium chloride)  5) KCl(potassium chloride)
8:ZnSO4(zinc sulphate)       &  1) HCOONa(sodium formate)      2) HCOOK(potassium formate)
9:HCOONa(sodium formate)     &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl(sodium chloride)  5) KCl,(potassium chloride)
10:HCOOK(potassium formate)  &  1) NH4Cl(ammonium chloride)    2) MgCl2(magnesium chloride)  3) CaCl2(calcium chloride)  4) NaCl                   5) KCl
11:HCOONa                    &  1) HCOOK.