Matt's plan is to kidnap the Reyes Cartel's daughter, frame it as the work of a rival cartel, and then "drop" her in the rival cartel's territory to trigger a war.
However, after the plan goes awry, Matt finally announces that he'll rescue Isabel and then put her in "witness protection." How can he officially apply for witness protection when his superiors have already ordered a cleanup to cover up this "incident"?
Even if the witness protection stemmed from the anger over losing a friend, what are his plans after rescuing Isabel? Will he drop her off again as originally planned, or will he just lock her up in an unofficial safehouse? There's no clue. Even the very act itself would have completely ruined his CIA operative career without a Plan B, and there's no explanation for it unless he's determined to retire. Should we consider this a plot hole?