Probably the Heavensward patches; almost everything from Antitower-onwards is such a relentless conga line of misery and trauma for both of them that it nearly drove them apart. Not helping matters was Mr. "You would go alone" setting off his girlfriend's abandonment issues by implying that he would have been willing to go with Minfilia to the First and leave Rahela behind… Things between them start to somewhat go back to normal towards the end of Stormblood… and then Thancred gets soulsnatched :'D