I remember in a solid state chemistry MOOC I took, from a professor who was a lithium battery researcher, the professor did mention in passing that we actually don't have a really good understanding of lithium batteries.
Of course he was talking about a much lower level than you need to understand when it comes to actually using them.
There are actually a lot of things we know how to deal with when it comes to engineering but have a poor grasp of the low level details. There was a great example in the Feynman Lectures where he says this about friction (Volume 1, section 12-2):
> It is quite difficult to do accurate quantitative experiments in friction, and the laws of friction are still not analyzed very well, in spite of the enormous engineering value of an accurate analysis. Although the law F=μN is fairly accurate once the surfaces are standardized, the reason for this form of the law is not really understood. To show that the coefficient μ is nearly independent of velocity requires some delicate experimentation, because the apparent friction is much reduced if the lower surface vibrates very fast. When the experiment is done at very high speed, care must be taken that the objects do not vibrate relative to one another, since apparent decreases of the friction at high speed are often due to vibrations. At any rate, this friction law is another of those semiempirical laws that are not thoroughly understood, and in view of all the work that has been done it is surprising that more understanding of this phenomenon has not come about. At the present time, in fact, it is impossible even to estimate the coefficient of friction between two substances.
That was written around 60 years ago. Anyone here happen to know if it still holds?