Assembly language and compiled languages
Well, it relates a bit to your question, indeed. The point is that compilers produce inefficient machine code at times for various reasons, such as not being able to completely analyze your code, inserting automatic range checks, automatic checks for objects being null, etc.
On the other hand if you write assembler code by hand and know what you're doing, then you can probably write some things much more efficient than the compiler, although the compiler's behavior may be tweaked and you can usually tell it not to do range checking, for example.
Most people, however, will not write better assembler code than a compiler, simply because compilers are written by people who know a good deal of really weird but really cool optimizations. Also things like loop unrolling are usually a pain to write yourself and make the resulting code faster in many cases.
While it's generally true that everything that a computer executes is machine code, the code that runs differs greatly depending on how many abstraction levels you put between the machine and the programmer. For Assembler that's one level, for Java there are a few more ...
Also many people mistakenly believe that certain optimizations at a higher abstraction layer pay off at a lower one. This is not necessarily the case and the compiler may just have trouble understanding what you are trying to do and fail to properly optimize it.
Assembly may sometimes be faster than a compiled language if an assembly programmer writes better assembly than that generated by the compiler.
A compiled language is often faster than assembly because programmers who write compilers usually know the CPU architecture better than programmers who are utilizing assembly in a one-off, limited-case, situation.
An assembly expert may be able to write assembly code that is more effective (fewer instructions, more efficient instructions, SIMD, ...) than what a compiler generates automatically.
However, most of the time, you're better off trusting the optimizer of your compiler.
Learn what your compiler does. Then let the compiler do it.