The YouTube shooter had a run-in with cops just hours before she opened fire at the media company's headquarters -- but they apparently thought nothing was amiss.

Nasim Aghdam's father, Ismail Aghdam, says he and his family had reported his daughter missing in Southern California before police in Mountain View, CA -- about 30 miles from YouTube HQ -- contacted them early Tuesday morning. 

He says cops told him she'd been found and everything was "under control" -- despite Ismail claiming he'd initially told authorities she might go to YouTube because she "hated" the company for allegedly censoring her videos.

Mountain View police confirm officers encountered Aghdam Tuesday asleep in her car in a parking lot. They ran her plates and found it matched the description of a missing person, and when officers made contact ... they concluded all was well, notifying her family.

Hours later, she shot and injured 3 people at the YouTube campus before killing herself.