At least they have some ideas...
From someone called a boffin but not in this field (thankfully!), the abstract - not behind the paywall - says:
"We also present new stable isotope measurements from the western equatorial Pacific that, in conjunction with previously published data5, 6, 7, 8, 9, 10, reveal a long-term trend of thermocline shoaling in the equatorial Pacific since ~13 Myr ago. We propose that a relatively deep global thermocline, reductions in low-latitude gradients in sea surface temperature, and cloud and water vapour feedbacks may help to explain the warmth of the late Miocene. Additional shoaling of the thermocline after 5 Myr ago probably explains the stronger coupling between pco2, sea surface temperatures and climate that is characteristic of the more recent Pliocene and Pleistocene epochs"
Seriously folks, this is how science works - you observe something unexpected, you come up with ideas to explain it, then test those ideas in the future.
Just like trying to understand why Venus is so much hotter than it should be...hey, what's all that CO2 doing there?
Couldn't find a picture of my old physics teacher here, so Prof. McGubbins will have to do.