Two separate issues seem to be affecting the FR-S only, even though it is built on the same line with the BRZ. Toyota issued "tech tips" to dealers to let them know that owners have reported that condensation has been forming inside the taillamp housings. According to an exchange on the FT86Club forum, the coupe's chief engineer declared that problem fixed after remedying a detail in the production process.
Another tech tip regarding body panel issues read, "Some 2013 Scion FR-S vehicles may exhibit a condition where body panel fitting may not meet customer expectations." It refers to complaints that panels were as much as a quarter-inch out of flush. It isn't clear how many cars are affected, nor how many owners have formally complainted, but according to a post on TundraHeadquarters.com, Toyota is "looking into it."