Agriculture is unlikely, as we would see a few species of plants and animals suddenly undergo a very rapid spread over an extremely small time period with no seemingly obvious reason to do so normally.
If you're not finding the strata with the fossils themselves you're not finding the strata of the associated agriculture.
Also even if you did, it would be extremely hard to differentiate normal explosive evolutionary radiation from adoption of agriculture.
Furthermore, time resolution of fossils from those periods of a few hundred of thousand years is considered "extremely precise"; that's dozens if times longer than agriculture has existed so far, which is about 10,000 years max.
You don't see "plants and animals suddenly undergo a very rapid spread over an extremely small time". You just see the "before" and "after" pictures, and only if you're very lucky you might get the "just before" and "just after" pictures.
tl;dr agriculture would only be marginally easier to detect than stone age hunter-gatherers. Most of that would be the effect of higher population densities, not so much than artefacts would be more identifiable per se.
I feel that people really overestimate the completeness of the fossil record. Talk of "gaps" and "missing links" might give the idea that if it's a film reel, only some frames are missing here and there; when the reality is the inverse, we have a handful of frames and everything in between is extrapolatedoing filling in. So if there is an unexpected scene in the movie, you won't know it exists if you didn't have the luck to catch a couple of pictures from it.
To go back to the OP and make an observation:
The present configuration of continents is such that all except one are either touching each other or only separated by short stretches of water, making humans spreading to theme possible.
Generally under the Mesozoic continents were more isolated. And sea levels higher.
A continental or subcontinental species is much less likely to be detected than a global one.
So if it evolved in such a configuration of continents that it could not reach others without oceanic navigation, it'd be much more easy to miss.