I'm not sure it is fair to call that a wart. Back when JCL was designed, C/C++ didn't exist yet, and nobody used "//" as a comment syntax. (C's predecessor BCPL introduced // comments, but it was designed in 1967, and OS/360 was already shipping to customers in 1966; C itself was designed in 1972, and initially it didn't have // comments; C++ borrowed them from BCPL in the 1980s, and then C borrowed them back from C++ after that.)

A more obvious example of a wart would be how it exposes low-level details of disk layout (e.g. space allocation in cylinders and tracks), which improved performance and simplified implementation back in the 1960s, but which nowadays is just useless complexity–modern disks have completely different physical layout, and you have to buy expensive mainframe-specific SAN controllers which know how to simulate the ECKD physical layout of legacy mainframe disks on top of modern industry standard disks/SSDs.