First you should confirm that the two nodes currently have the same chain. This can be done easily by checking that the output of getlastblockinfo is the same on each. If the hash matches, so much the entire chain.
Assuming yes, then take a look at the blocks that differ between the two nodes. It is possible that there was some temporary non-consensus across the network, in which case a block might have been included in one node's chain but not in another's. This is not a cause for concern since the network automatically re-establishes consensus, unwinding a block and including another one where necessary. You can query any particular block using the getblock API with its hash – if confirmations=-1 then it's not on the active chain.