Actually, this sounds (from the article) like the EIR and/or the various permits had mitigation measures, which included timing of construction wrt kit fox (they settle while having kits, then may leave). The construction contractor didn't quite follow the rules exactly. This is nothing new; dealing with endangered species is simply part of the job for big projects, especially in the SJV with the kit fox. It's not unique to HSR.

Road projects in the SJV have dealt with it for years - in one case I heard of, the median of the SR99 freeway was "critical habitat" due to kit fox tracks found there, which required some expensive mitigation for a widening job. Same thing with certain birds and bats on bridges - if they're present (and in the Valley they usually are, in season) you either can't work until they leave or have to follow some very picky rules about mitigation and relocation. Contractors sometimes mess these things up if they aren't familiar with everything and aren't closely monitored.

Bottom line: this is a construction oops that will require reeducation of some people and payment of various penalties. It happens to everybody, especially the first couple of times they work in the area. If the agency keeps on top of the contractor, it shouldn't happen again.

*Good judgement comes from experience. Experience comes from bad judgement.*