OK, here is an example. Let's consider 'memcpy'. There are various problems with implementing memcpy in C:
1) You can't assume that pointers are aligned.
2) (related) If the user asks for you to copy n bytes, you better not read byte n+1, even if you don't need it, because maybe it is on a different page which is not available for reading.
So, an optimised memcpy usually first has to do a bit of work to find the 'aligned segment', do that, topped and tailed with some special cases.
A JIT compiler for Javascript (for example) takes issues of alignment out of the hands of the user, so can make any assumptions it wants by keeping such choices away from users.
Of course, we could write a memcpy_aligned (and some systems have such a method), but we can't ever optimise simple memcpy as much as the equivalent in javascript.