Often internal tuners are automatic -- that is, they initiate a retune sequence when the SWR drifts too high, usually above some settable threshold or something like above 2:1.
If you are using an internal tuner with an external tuner (which is OK if done right) then you could have problems if the internal tuner is enabled for automatic mode. What may happen is that as you adjust the external manual tuner, you may affect the SWR that the internal tuner sees and it will change automatically as a result. This change though on the internal tuner can affect the external tuner as well. It is even worse if the external tuner is also an automatic tuner. Thus, internal tuners can battle with external tuners in an never ending war of attempting to get a good match.
Usually, a tuner expects input side to be 50 ohms and therefore you should present a 50-ohm impedance to the external tuner by disabling your internal tuner. This is the smart thing to do. Life is simpler with only one tuner being active.