They leant later that Chief Naga had been educated at Oxford University some years before.

这是一般过去时和过去完成时。
they learnt(他们了解到)这一动作发生在过去，所以用一般过去时，而Chief Naga受教育这一动作则发生在“they learnt(他们了解到)”这一动作之前，即发生在过去的过去，所以用过去完成时，并且是过去完成时的被动态，即had been educated。