Astronomical radio emission is typically much weaker compared to ambient (terrestrial) emission, e.g., emission by the atmosphere, the telescope, the surroundings, and the receiver, so one needs to clean the measured signal from these contributions. (Fun fact: a typical radio dish even collects some emission from behind the telescope.)
In single-dish observations, this is done by observing a position as close to the target source as possible and subtracting this OFF emission from the ON emission. Assuming that both lines of sight are similarly affected by all local error contributions, this leaves the source's emission. This requires the OFF to be emission-free, which is surprisingly hard depending on the observed frequency. Imagine you want to observe molecular emission from a giant molecular cloud. Molecules form once they are sufficiently shielded from harmful UV radiation, so pointing away from the cloud should do the trick unless you accidentally hit a different cloud that happens to be in the foreground or background. (There are many interstellar clouds in the Milky Way. If you choose an OFF that is too far away, you may end up with a line-of-sight that passes different atmospheric (terrestrial) volume elements with slightly different emissions. This will lead to a worse ON-OFF correction.
The MeerKAT data is from an interferometric observation which do not rely on ON-OFF but gets rid of all contaminations by deconvolution followed by an absolute flux calibration using a particular calibration target PKS B1934-638 (Details: Heywood et al. 2020 ).
All these data reduction procedures are imperfect, given that any signal sufferers from systematic (and stochastic) noise. Therefore, it is not uncommon that the reduced and calibrated date shows some (low) negative flux values. In this case, we are talking about 1e-3 relative to the peak flux. In other words, -0.4 mJy/beam is still zero emission.
For complex gain calibration at the NRAO see here: https://science.nrao.edu/facilities/vla/docs/manuals/obsguide/calibration and this PDF. If you are interested in single-dish fulx calibration there is a manual from the IRAM 30-m. There is a nice description of all steps from the Lab Course M at I. Physics Institute of the Universität zu Köln: Manual