Probably because bad code that you create initially without thinking that it's a core piece of your stack becomes depended on for its crappy behavior, and then you can't change much without breaking workflows.
I seem to recall Fred Brooks talking about that experience with OS/360 JCL (maybe just straight up in The Mythical Man Month?).
If agents really are superpowerful at programming tasks why not just have it rewrite the tool that the majority of your customers use and have it recreate the bugs? I mean presumably its the primary force behind the current version so what's the major cost there?