Quantifying Spectroscopic Flux Variations Between JWST NIRISS and NIRSpec: Slit Losses in Emission Line Measurements of z$\sim$1-3 Galaxies

We analyze JWST NIRISS and NIRSpec spectroscopic observations in the Abell 2744 galaxy cluster field. From approximately 120 candidates, we identify 12 objects with at least a prominent emission lines among \Oii, \Hb, \Oiiia, \Oiiib, and \Ha that are spectroscopically confirmed by both instruments. Our key findings reveal systematic differences between the two spectrographs based on source morphology and shutter aperture placement. Compact objects show comparable or higher integrated flux in NIRSpec relative to NIRISS (within 1$\sigma$ uncertainties), while extended sources consistently display higher flux in NIRISS measurements. This pattern reflects NIRSpec’s optimal coverage for compact objects while potentially undersampling extended sources. Quantitative analysis demonstrates that NIRSpec recovers at least $63\mathrm{\%}$ of NIRISS-measured flux when the slit covers $>15\mathrm{\%}$ of the source or when $R_e<1$kpc. For lower coverage or larger effective radii, the recovered flux varies from $24\mathrm{\%}$ to $63\mathrm{\%}$. When studying the \Ha/\Oiiib emission line ratio, we observe that measurements from these different spectrographs can vary by up to $\sim$0.3 dex, with significant implications for metallicity and star formation rate characterizations for individual galaxies. These results highlight the importance of considering instrumental effects when combining multi-instrument spectroscopic data and demonstrate that source morphology critically influences flux recovery between slit-based and slitless spectroscopic modes in JWST observations.