measuring ... at the switching node of the converter
But If I measure it separately, I am able to get the correct ripple voltage amplitude
The switching node of the converter is very sensitive to any additional capacitance loading. Even the small capacitance of a scope probe (use a 10:1 probe to get the smallest capacitance!) is enough to influence the behavior.
You might think, well this is only 248 kHz so it's not that high in frequency. That is correct but that 248 kHz signal is not a sine wave. Ideally it's more like a square wave with very sharp edges (due to fast switching which is needed for good efficiency, low switching losses). Such a square wave has harmonic frequencies content up to very high frequencies, like up to 1 GHz or higher. At such frequencies, any additional capacitance and inductance does make a difference!
In a non-synchronous DCDC down converter there will be a Schottky diode between the switching node and ground. The capacitance of this diode influences the behavior of the converter even though this capacitance can be quite small depending on the diode that is used. When you probe the switching node you add some capacitance in parallel with this diode.
For an accurate ripple measurement, only probe at the output and probe directly across the filter capacitor at the output.
