I think the consensus is that you can use the glitch to boost his affection, and the trophy pops by looking for his affection level to be within a certain range. If you overuse the glitch, or your affection level is already high enough, and you boost it just a little too much to go past the high-end of the affection range the trophy is looking for, it will cause the trophy not to pop.
tl;dr - if you're going to use the cosmo canyon glitch, don't overdo it.
Yeah i can confirm this, i got him up to around 35, but the girls were still in the low 40s. I did the trick 7 times to get him to the mid 50s and it popped for me