Shelby started her mission on the Enterprise by questioning orders from a superior officer and then went down to the planet against orders without letting commanding officer know about it.
Not really. Her 1st scene is with Admiral Hanson, who lets it be known he intends to carry on with the mission by granting her a "wide latitude" in order to "Get things done". That is the tone which he set. She's a mission specialist with some liberty to call her own shots
She doesn't question anybody's orders right off. What she does is make the call to go early. She wasn't shown being ordered off the planet until Riker joined her. She was simply instructed that he'd be coming along
with Laforge & Data. She just took Data & went sooner, because before Riker & Laforge became available, storm fronts altered the conditions, & jeopardized her research
She took the initiative to improvise a command decision, while other, higher ranking officers were unavailable, & frankly, that's exactly the kind of thing Hanson said she'd be doing. We're not even really certain she is a direct subordinate to Riker, such that she is tied down to his schedule. Riker just didn't like it, because he felt his toes being stepped on by the person who'd announced an interest in his job. So, he pulled rank on her, & she apologized & noted it for future reference
You'll recall that remark Hanson made to Picard about Riker looking like he's standing still, alongside up and coming officers? This is what that looks like. She'd already figured everything out by the time he got his butt down there, but ultimately, all she did was move up his time table, due to changing conditions
Unlike Riker
holding back Jellico's time table by refusing to carry out a change in crew allotment, because he didn't agree with it. In both cases, Riker expects he has final say, & while he does in Shelby's case (It would appear) she too has been granted certain liberties by the admiral that brought her, so it's at least understandable & forgivable to assume she might make a misstep & someone's tender little toes might get in the way