I've had trouble melting the housings of the xt pin connectors when soldering, so the contacts go all wonky and don't fit the other connector any more... I guess that's what you've had too?

It can help to mate the connector you're working on with a spare connector, that keeps the contacts lined up and works as a bit of a heat sink...

... Though there's also the risk you ruin two connectors not one.... :'(