Yes, depending on the type of seed, many scenarios could be manifesting:
--- Rick's suggestion above, where seeds rotted.
--- seeds might begin germinating, but then die due to inadequate constant moisture.
--- many species naturally have low viability rates, for instance many members of the Aster family (Asteracae/Compositae) - not just Aster species. In such a case, the soggy seeds would already be dead.
--- many species require pollination from a plant of the same species but different genetics. In other words, they can't pollinate themselves (or clones of the same plant cannot pollinate each other). Here, all "seeds" would be dead (actually never developed).
--- flowers may never have been pollinated properly from the start, due to inclement weather or lack of the right pollinating fauna. Here again, empty seeds often develop.
--- many sterile plants still produce what looks like viable seed.
I'm sure there are many more possibilities. It must happen occasionally, when pods (or whatever) do rot as you surmise, but we always need to be looking at all the probabilities.
