All of this is avoidable and the problems are self-inflicted. While many people hate compliance overlay software such as Concur, it can also be programmed to eliminate options which are not acceptable to the employer.
These can include Spirit (safety), WN (no interlining), BE fares, and the like. Smarter employers also flag non-compliant tickets for review, but don't stop the ticketing.
When the same employee is routinely spending more and producing less, that is someone to get rid of. But, the same employee who produces on the road ---- who cares if that guy spends an extra $500 or so?