The reasons for primer dimer formation in a NTC are often due to multiple factors. These include: sub-optimal primer annealing temperature (often due to differences in buffering conditions between different qPCR kits), sub-optimal primer synthesis (HPLC purified primers result in less primer dimer formation and are useful for low copy number detection), and poor primer design (using software such as Primer3 is recommended in primer design).
Reducing the total number of cycles in a qPCR reaction is an alternative method if amplification of the primer dimer lies outside of the range of the experimental data. For example, if the sample being interrogated has a Cg of 28 cycles, contains specific product only (no primer dimer), and the NTC amplifies a primer dimer after 37 cycles, the reaction can be run for 35 cycles, rather than 40. This approach can be taken only when the sample being tested gives rise to specific product and not a combination of specific product and primer dimer.