Maybe some people think of the Chie and Yukiko thing because Chie is a bit of a tomboy girl and since they are close friends well, we start imagining things.Yukiko refers to Chie as a "Prince" several times...
That's pretty obviously a metaphorical reference. Chie was Yukiko's only out in terms of her various family problems and duties, her friendship with Chie gave her a reason to keep going, just like how the prince saves the princess in a fairy tale.
I guess people are just stupid and want to see homoeroticism so badly in everything that they turn a blind eye to the exceedingly obvious. Just like with Kanji. The game freaking TELLS you he's not gay, the whole problem was that he was afraid that his "girly" hobbies of being interested in textiles and sewing/knitting would get out and that people would make fun of him for it. He THINKS that because he likes a "girly" hobby that he might be gay, but then realizes through his confrontation with his shadow self that the real problem is rooted deeper and he comes to terms with himself. It's really not a very complex issue and I thought the game did an excellent job of explaining everything to the player, but people just get incredibly stupid when it comes to stuff like this.
The "Yousuke might be gay" thing probably comes from a misinterpretation of an early developer interview where it was stated that you could get into a relationship with Yousuke. They were really just talking about the fact that you could have S.Links with all the male party members, but it was initially translated as that you could date them and a lot of people fell for it. See also: fangirls like the homosex.