Global and regional methane budgets are markedly uncertain. Conventionally, estimates of methane sources are derived by bridging emissions inventories with atmospheric observations employing chemical transport models. The accuracy of this approach requires correctly simulating advection and chemical loss such that modeled methane concentrations scale with surface fluxes. When total column measurements are assimilated into this framework, modeled stratospheric methane introduces additional potential for error. To evaluate the impact of such errors, we compare Total Carbon Column Observing Network (TCCON) and GEOS-Chem total and tropospheric column-averaged dry-air mole fractions of methane. We find that the model’s stratospheric contribution to the total column is insensitive to perturbations to the seasonality or distribution of tropospheric emissions or loss. In the Northern Hemisphere, we identify disagreement between the measured and modeled stratospheric contribution, which increases as the tropopause altitude decreases, and a temporal phase lag in the model’s tropospheric seasonality driven by transport errors. Within the conte ... mehrxt of GEOS-Chem, we find that the errors in tropospheric advection partially compensate for the stratospheric methane errors, masking inconsistencies between the modeled and measured tropospheric methane. These seasonally varying errors alias into source attributions resulting from model inversions. In particular, we suggest that the tropospheric phase lag error leads to large misdiagnoses of wetland emissions in the high latitudes of the Northern Hemisphere.