The issue here is that you are trying to do straight arithmetic when for an _exact_ result you need to do vector math. You've simple stumbled into one of the corner cases where the difference between the simple arithmetic and the vector math result is quite large.
When you have a large panel with lots of loads, the vector math issues tend to average out. So when you do a panel schedule a perfectly reasonable approximation is to assign a simple arithmetic VA value to each load connected to a phase, add up all the VA values for each phase, and call that the VA placed on that phase. This is generally a good enough approximation, but it is _not_ exact.
In the OP's case, to do an exact calculation not only would you need to know the amp rating of the load, you would also need to know the phase angle of the load. But for the sake of discussion, I will assume that the load is a perfect resistor. I will further assume that this is the _only_ load placed on the transformer supplying the 120/208V. In this case the load is 50*208 = 10.4 kVA just as originally calculated.
As Charlie says, 50A flows from phase A through the load to phase B. Since the phase A coil is providing 120V and is seeing 50A, the load on that coil is 6kVA. Similarly the load on coil B is 6kVA. This is a total of 12kVA transformer loading! Sounds like a paradox. The load is a pure resistor with a power factor of 1, consuming 10.4 kVA (and thus 10.4 kW) but the transformer loading is 12 kVA.
What is happening is that even though the current through the load is flowing in phase with the A-B voltage, the current through the transformer coils is _not_ flowing in phase with their respective N-A and B-N voltages. In the transformer coils there is a power factor less than 1.
To do a more accurate panel schedule, instead of assigning a VA value to each load/phase you would assign a current vector (current magnitude in amps and phase angle in degrees). Then for each phase you would do the vector sum of all of these current values, to get the total current flowing on each phase.
Even this would not be perfectly accurate, but it would be a closer result. However in general the simple arithmetic sum of load VA values is accepted as good enough, unless you look at the corner cases of extremely unbalanced loading.
-Jon