I had a similar gap on a rafter-post connection and, as I recall, we did do a fit-up. We tried to pull the joint together (in-situ), and with all kinds of come-alongs and commanders could not get it together. The peg holes were drilled with a slight draw but there was no way to get the peg started. Unless....a really off-center, long taper on the peg. It worked and went in like it was planned that way. The joint tightend up beautifully.
Is it possible that a draw bore was accidentally drilled the wrong way (a PUSH bore) on your frame? It certainly wouldn't the first time we've seen that!