Rather than allow the employee to use the common women's restroom, the employer required her to use a single-use restroom (the employer claims the employee collaborated on this plan). The EEOC held that denying the employee use of the common women's restroom was disparate treatment on the basis of sex in violation of Title VII. To get there, the EEOC had to hold that the bathroom denial rose to the level of "adverse employment action" - a call that could easily go either way.
Also, the employee's team leader continued to occasionally refer to her by her male name, using male pronouns, and often calling her "sir." The EEOC concluded that this was sex-based harassment. Whether these incidents constituted "severe or pervasive" harassment (a requirement for harassment claims) was another close call.
Clearly, the EEOC has gone all-in on utilizing Title VII to protect transgender employees from workplace discrimination. Whether courts will address these issues in the same manner remains an open question.