I have been running some benchmarks on some algorithms and profiling their memory usage and efficiency (L1/L2/TLB accesses and misses), and some of the results are quite intrigu
First, inclusive cache hierarchies may not be so common as you assume. For example, I do not think any current Intel processors - not Nehalem, not Sandybridge, possibly Atoms - have an L1 that is included within the L2. (Nehalem and probably Sandybridge do, however, have both L1 and L2 included within L3; using Intel's current terminology, FLC and MLC in LLC.)
But, this doesn't necessarily matter. In most cache hierarchies if you have an L1 cache miss, then that miss will probably be looked up in the L2. Doesn't matter if it is inclusive or not. To do otherwise, you would have to have something that told you that the data you care about is (probably) not in the L2, you don't need to look. Although I have designed protocols and memory types that do this - e.g. a memory type that cached only in the L1 but not the L2, useful for stuff like graphics where you get the benefits of combining in the L1, but where you are repeatedly scanning over a large array, so caching in the L2 not a good idea. Bit I am not aware of anyone shipping them at the moment.
Anyway, here are some reasons why the number of L1 cache misses may not be equal to the number of L2 cache accesses.
You don't say what systems you are working on - I know my answer is applicable to Intel x86s such as Nehalem and Sandybridge, whose EMON performance event monitoring allows you to count things such as L1 and L2 cache misses, etc. It will probably also apply to any modern microprocessor with hardware performance counters for cache misses, such as those on ARM and Power.
Most modern microprocessors do not stop at the first cache miss, but keep going trying to do extra work. This is overall often called speculative execution. Furthermore, the processor may be in-order or out-of-order, but although the latter may given you even greater differences between number of L1 misses and number of L2 accesses, it's not necessary - you can get this behavior even on in-order processors.
Short answer: many of these speculative memory accesses will be to the same memory location. They will be squashed and combined.
The performance event "L1 cache misses" is probably[*] counting the number of (speculative) instructions that missed the L1 cache. Which then allocate a hardware data structure, called at Intel a fill buffer, at some other places a miss status handling register. Subsequent cache misses that are to the same cache line will miss the L1 cache but hit the fill buffer, and will get squashed. Only one of them, typically the first will get sent to the L2, and counted as an L2 access.)
By the way, there may be a performance event for this: Squashed_Cache_Misses.
There may also be a performance event L1_Cache_Misses_Retired. But this may undercount, since speculation may pull the data into the cache, and a cache miss at retirement may never occur.
([*] By the way, when I say "probably" here I mean "On the machines that I helped design". Almost definitely. I might have to check the definition, look at the RTL, but I would be immensely surprised if not. It is almost guaranteed.)
E.g. imagine that you are accessing bytes A[0], A[1], A[2], ... A[63], A[64], ...
If the address of A[0] is equal to zero modulo 64, then A[0]..A[63] will be in the same cache line, on a machine with 64 byte cache lines. If the code that uses these is simple, it is quite possible that all of them can be issued speculatively. QED: 64 speculative memory access, 64 L1 cache misses, but only one L2 memory access.
(By the way, don't expect the numbers to be quite so clean. You might not get exactly 64 L1 accesses per L2 access.)
Some more possibilities:
If the number of L2 accesses is greater than the number of L1 cache misses (I have almost never seen it, but it is possible) you may have a memory access pattern that is confusing a hardware prefetcher. The hardware prefetcher tries to predict which cache lines you are going to need. If the prefetcher predicts badly, it may fetch cache lines that you don't actually need. Oftentimes there is a performance evernt to count Prefetches_from_L2 or Prefetches_from_Memory.
Some machines may cancel speculative accesses that have caused an L1 cache miss, before they are sent to the L2. However, I don't know of Intel doing this.