Turn the time back a little when the Mechanoids first started fighting with their respective Mechanoids, Jin had just teleported the Mecha Gigan Dragon via his Dungeon Instance creation technique. The reason why he did not do it immediately was mainly because he did not expect such a huge dragon to come out to play with the rest.
He assumed that the Mecha Dragons were mostly 1st tier and a few 2nd tier to populate the battlefield. Never did he think that all were 2nd tier Mecha Dragons and the one he was fighting had to be a 3rd tier. Thus, the dungeon instance that he had prepared was not valid for use against the Mecha Gigan Dragon.