Yes, the president ordered the pentagon to 'study the issue' which gives him sufficient latitude to take his time in ordering, overseeing and analyzing the results of the study, so he isn't forced to go through the ranks and disrupt ongoing deployments in a pointless, expensive hunt at the snap of a finger.
He's not disobeying the order, he's just putting it on a slower timetable than Agent Orange is likely to have envisioned because the president is an impatient baby who wants everything now, now now.
Source? By all accounts, Mattis ordered the study and the freeze on letting trans recruits in in the first place after plans were already in motion to let trans recruits in from the Obama administration
https://www.nytimes.com/2017/06/30/us/pentagon-delays-transgender-recruits.html?mcubz=3
JUNE 30
A plan to allow transgender recruits to join the United States military beginning on Saturday has been delayed for six months by Defense Secretary Jim Mattis, a Pentagon spokeswoman said on Friday.
The 11th-hour decision byMr. Mattis will allow service leaders to ”review their accession plans and provide input" as they consider what impact adding transgender recruits would have on ”the readiness and lethality of our forces," the spokeswoman, Dana W. White, said in a statement.
The delay was announced one year after the Pentagon lifted its ban on transgender people serving openly in the armed forces.
Military leaders formally requested last week that Mr. Mattis approve a delay, The Associated Press reported on Friday. The news agency quoted a memo it obtained in which the defense secretary noted that his decision to defer ”does not presuppose the outcome of the review."