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Context. Integral field spectroscopy (IFS) provides detailed information about galaxy kinematics at high spatial and spectral resolution, and the disentanglement of the gaseous and stellar components is a key step in the analysis of the data. Aims. We study how the use of several stellar-subtraction methods and line fitting approaches can affect the derivation of the main kinematic parameters (velocity and velocity dispersion fields) of the ionized gas component. Methods. The target of this work is the nearby galaxy NGC 2906, observed with the MUSE instrument at the Very Large Telescope (VLT). A sample of twelve spectra is selected from the inner (nucleus) and outer (spiral arms) regions, characterized by different ionization mechanisms. We compare three different methods to subtract the stellar continuum (FIT3D, STARLIGHT and pPXF), combined with one of the following stellar libraries: MILES, STELIB and GRANADA+MILES. Results. The choice of the stellar-subtraction method is the most important ingredient affecting the derivation of the gas kinematics, followed by the choice of the stellar library and by the line-fitting approach. In our data, typical uncertainties in the observed wavelength and width of the Hα and [NII] lines are of the order of ⟨δλ⟩rms ∼ 0.1 Å and ⟨δσ⟩rms ∼ 0.2 Å (i.e., ∼5 and 10 km s−1, respectively). The results obtained from the [NII] line seem to be slightly more robust, as it is less affected by stellar absorption than Hα. All methods considered yield statistically consistent measurements once a mean systemic contribution Δλ¯ = Δσ¯ = 0.2 ΔMUSE Δ λ ¯ = Δ σ ¯ = 0.2 Δ MUSE $ \Delta \bar\lambda = \Delta \bar\sigma = 0.2\,\Delta_{\mathrm{MUSE}} $ is added in quadrature to the line-fitting errors, where ΔMUSE = 1.1 Å ∼50 km s−1, which denotes the instrumental resolution of the MUSE spectra. Conclusions. Although the subtraction of the stellar continuum is critical in order to recover line fluxes, any method (including none) can be used to measure the gas kinematics, as long as an additional component, Δλ¯ = Δσ¯ = 0.2 ΔMUSE Δ λ ¯ = Δ σ ¯ = 0.2 Δ MUSE $ \Delta \bar\lambda = \Delta \bar\sigma = 0.2\,\Delta_{\mathrm{MUSE}} $ , is added to the error budget. [ABSTRACT FROM AUTHOR]