I am heterozygous for a SNP and it seems better/worse than being homozygous for the mutation. Is this a mistake?

No, it is not a mistake. What you are witnessing is called ""molecular heterosis" and it appears counter-intuitive at a molecular level. For example, if homozygous wild type (AA) has “normal” gene expression, and a mutation (B) decreases that expression, then heterozygotes (AB) would be expected to have an intermediate effect on expression and homozygotes (BB) for the mutation should show the greatest decrease. In fact, sometimes this is not the case as AB may show the greatest change. When individuals heterozygous for a specific genetic polymorphism show a significantly smaller effect (negative heterosis/underdominance) or greater effect (positive heterosis/overdominance) for a trait than those homozygous for either allele, this is heterosis.
Geneticists have several theories for this observation. 1. There exists an unknown, independent factor at play causing a hidden difference in how the genotypes express. 2. The goldilocks theory: an inverted U-shaped response curve in which either to little or too much gene expression is harmful and optimal gene expression occurs in heterozygotes (positive heterosis). 3. Heterozygotes are potentially genetically more fit due to a broader range of gene expression than AA or BB homozygotes. AB genotypes have more resiliency, or plasticity, in other words: more flexibility to respond to change.(positive heterosis), or actually the opposite can occur: AB is the less desired combination genetically compared to AA or BB.