Sorry I didn’t answer this sooner- I was on mobile all weekend and it wouldn’t let me tag it which I need to do because here there be SPOILERS.
Okay, the episode where Jensen mentioned Dean crying is 11×21, titled All in the Family. Originally, he just mentioned that he let a tear fall because it felt right in a scene with himself, Jared, and one other actor. As usual, many people assumed that had something to do with Castiel. In truth, Jensen later said in a M&G that the other actor is Rob Benedict. Jared confirmed it later and said that it was about their parents’ deaths. It has nothing to do with Cas.
I know some people find all the chatter and theories about Destiel upsetting but please keep in mind that this happens every season. We get to the last month or two before hiatus and rumors start flowing that this is the year that Destiel becomes canon. In season 9, they said Cas was Dean’s Colette and he would save Dean from his fate just by asking him to stop like Colette did with Cain. Didn’t happen. In season 10, they said that Cas was going to be the one who cured Dean of the Mark and some even said that a Destiel kiss was confirmed for the last scene. Remember when that totally happened? Nope. Me neither.
What I’m trying to say here is that shippers enjoy theorizing about this stuff and writing meta and that’s fine. I have an English degree and I spent a huge amount of time in college coming up with theories about fictional characters. It’s a thrill to find something new to say and toss it out to others and start a conversation, even if those ideas end up being way off base and probably nothing like what the original author intended. Please don’t let this stuff bother you or make you avoid episodes of a show you love. It’s all just conjecture wrapped up in shipping wishes.