Thermal emission from cold dust grains in giant molecular clouds can be used to probe the physical properties, such as density, temperature and emissivity in star-forming regions. We present the SCUBA-2 shared-risk observations at 450 $mu$m and 850 $mu$m of the Orion A molecular cloud complex taken at the James Clerk Maxwell Telescope (JCMT). Previous studies showed that molecular emission lines can contribute significantly to the measured fluxes in those continuum bands. We use the HARP $^{12}$CO J=3-2 integrated intensity map for Orion A in order to evaluate the molecular line contamination and its effects on the SCUBA-2 maps. With the corrected fluxes, we have obtained a new spectral index $alpha$ map for the thermal emission of dust in the well-known integral-shaped filament. Furthermore, we compare a sample of 33 sources, selected over the Orion A molecular cloud complex for their high $^{12}$CO J=3-2 line contamination, to 27 previously identified clumps in OMC-4. This allows us to quantify the effect of line contamination on the ratio of 850 $mu$m to 450 $mu$m flux densities and how it modifies the deduced spectral index of emissivity $beta$ for the dust grains. We also show that at least one Spitzer-identified protostellar core in OMC-5 has a $^{12}$CO J=3-2 contamination level of 16 %. Furthermore, we find the strongest contamination level (44 %) towards a young star with disk near OMC-2. This work is part of the JCMT Gould Belt Legacy Survey.
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