It’s a known issue to Adobe with OSX 10.11 El Capitan. Google “Premiere Wandering Playhead”.
On the Adobe support website, an employee said it “might be” fixed on the next update. So get used to hanging around waiting for that playhead to catch up. I’m ready to downgrade to Yosemite to see if that fixes it. Because from the frequency of Adobe’s replies, it’s pretty clear that they have no intention of making this a priority, despite the fact that editors are losing precious time over this bug.