We demonstrated that some non-synonymous and synonymous mutations in $gyrA$ in $Mycobacterium\; tuberculosis$ result in systematic false-resistance results to fluoroquinolones using the Hain GenoType MTBDRsl assays (version 1 and 2) by preventing the binding of wild-type probes. Moreover, such mutations can prevent the binding of mutant probes, designed for the identification of specific resistance mutations. Although these mutations are likely rare globally, they occur in approximately 7% of multidrug-resistant tuberculosis strains in some settings.