A large eddy simulation is performed to study secondary tones generated by a NACA0012 airfoil at angle of attack of $\alpha = 3^{\circ}$ with freestream Mach number of $M_{\infty} = 0.3$ and Reynolds number of $Re = 5 \times 10^4$. Laminar separation bubbles are observed over the suction side and near the trailing edge, on the pressure side. Vortex shedding occurs aft of the suction side separation bubble, and vortex interaction results in merging or bursting such that coherent structures or turbulent packets are advected towards the trailing edge. This mechanism modulates the amplitude of the incident pressure signal, leading to different levels of noise emission. Despite the intermittent occurrence of laminar–turbulent transition, the noise spectrum depicts a main tone with multiple equidistant secondary tones. To understand the role of flow instabilities on the tones, the linearised Navier–Stokes equations are examined in their operator form through biglobal stability and resolvent analyses, and by time evolution of disturbances using a matrix-free method. These linear global analyses reveal amplification of disturbances over the suction side separation bubble. Spanwise-averaged pressure fluctuations elucidate aspects of the acoustic feedback loop mechanism in the nonlinear solutions. This feedback process is self-sustained by acoustic waves radiated from the trailing edge, which reach the most sensitive flow location near the leading edge, as identified by the resolvent analysis. Flow disturbances arising from secondary diffraction and phase interference among the most unstable frequencies computed in the eigenspectrum are shown to have an important role in the feedback loop.