While Pumpernickel's approach is interesting, I'd like to see a tweaked version of it.
First, have a flag for "placed" monsters - these would include ants and bees, vault monsters, and any other monsters that are generated immediately in position, rather than being randomly generated (including, for instance, the trees of the animated forest, wilderness encounters, etc).
Second, keep distinct counters for each of three (or is it four?) categories of monster - normal, summoned (is bred a separate flag?), and placed.
Now, placed monsters should still increase the strength of future monsters of the same type, but the effect should be reduced. For instance, perhaps the impact is only a quarter of the impact of normal monster kills. This would ensure that ants and bees grow slower, and that killing pre-set monsters like in single-type vaults doesn't lead to overly powerful monsters of the same type later - instead, it makes them more powerful, but to a lesser extent. The same idea would apply to the number of summoned/bred monster kills, but with other impact numbers. So, for instance, if we let the number of normal kills be N, placed kills be P, and summoned kills be S (assuming bred is same as summoned), then perhaps the formula is N + P/4 + S/8 - so it takes four placed kills or 8 summoned kills to be equivalent to the impact of one normal kill.
Summoned and bred monsters should operate on a different system. Their level should be dependent more on the level of the summoner/breeder that they came from, than on how many you have killed. However, they should still be influenced by number of kills of that type of creature. How to achieve this? Upon summoning or breeding, the system checks the level of the summoner/breeder, and uses this as a base value. It then uses a formula based on kills of the summoned/bred monster type to determine how much more or less powerful it is.
Let's use an example of a jackalwere. You have killed 5 jackals normally, 20 from a previous jackalwere, and 25 from a gnoll vault. My knowledge of exactly what the formulae are for power of generated monsters is limited, so I'll do this simplistically, as a simple linear level progression. Suppose that the current Jackalwere level is 5, and Jackalwere levels start at 4. Suppose that the jackal levels start at 1, and that they increase at a rate of one level every 4 normal jackals. Now, the total kills as far as level raises is concerned is 5 + 25/4 + 20/8 = 13.75, which equates to 3 raises in level, placing normal jackals on level 4. But what about the summoned jackals? Well, start with the jackalwere level, 5. Subtract 2 levels as the base level for its summons, so 3. Then add half the number of level raises the summoned creature has seen, in this case half of 3 works out to 1 (rounded down), resulting in level 4 summoned jackals.
This is, of course, just an example of what I mean, and not my suggestion for the best way to implement my idea. It serves to describe what I mean regarding the summoned monsters, not to be a specific design for how to implement it.