Observations of the dust emission using millimetre/submillimetre bolometer arrays can be contaminated by molecular line flux, such as flux from 12CO. As the brightest molecular line in the submillimetre, it is important to quantify the contribution of CO flux to the dust continuum bands. Conversion factors were used to convert molecular line integrated intensities to flux detected by bolometer arrays in mJy beam−1. These factors were calculated for 12CO line integrated intensities to the SCUBA-2 850 and 450 μm bands. The conversion factors were then applied to HARP 12CO 3–2 maps of NGC 1333 in the Perseus complex and NGC 2071 and NGC 2024 in the Orion B molecular cloud complex to quantify the respective 12CO flux contribution to the 850 μm dust continuum emission. Sources with high molecular line contamination were analysed in further detail for molecular outflows and heating by nearby stars to determine the cause of the 12CO contribution. The majority of sources had a 12CO 3–2 flux contribution under 20 per cent. However, in regions of molecular outflows, the 12CO can dominate the source dust continuum (up to 79 per cent contamination) with 12CO fluxes reaching ∼68 mJy beam−1.