mesh,
If you are able to take the feeder/transformer out of service for a time, you could do primary injection tests to confirm CT connections and ratios.
The exact details on how to do a primary injection test depends on how the CT's are connected but is generally as follows:
Put a temporary 3-phase short circuit on one side of the CT's (generally the "downstream" side). The short circuit needs to be short term rated to carry the current you are going to primary inject. In your case with 100/5 CT's you should look to inject 100A and you may be able to achieve this with a secondary test set. Put ammeters in each CT secondary and also in the CT residual circuit. Primary inject into one phase and return via another phase. If all is well, the ammeters in the CT secondaries corresponding to the phases you are injecting should read the same (the current should be injected current divided by CT ratio) and the ammeter in the CT residual circuit should read zero (or very close to it). Do the test for all three combinations i.e. in A out B, in A out C, in B out C. You will know you have found the problem if you get a high residual current reading. It helps if the ammeters are analogue type. The protective relay should remain in the circuit.
Prior to doing any work, be sure that safe and correct isolations are carried out and at the completion of the work be sure to re-instate the system to normal. Also be sure to use the services of a suitably experienced test engineer.
Any errors in CT connection or ratio become more noticeable at higher currents.
Regards