It appears that in random places, a few stones (7 so far i've spotted) in my fort won't register as usable (by workshops or for building things), [...]
It's not as simple as those stones already being earmarked for some other (possibly suspended, maybe just long-standing and yet still unfulfilled) construction project of some kind, is it?
Ensure all your resource pre-assigning stone-using jobs (workshops, et al, pick and choose at job-activating time, unless I'm very much mistaken) are not causing the problem. Cancelling any that are suspended and reapplying them is one thing I occasionally do when peculiar things happen (beware of getting two or more jobs mutually blocking each other by needing the material lying on the build square of another of the construction sites, suspending that job when attempted, etc, etc... I've had fun with something like that happening, in the past.
) Also it can help re-optimise the material paths, if done wisely after closer material supplies have been generated (or partially moved from A to B, but abandoned in a place fairly handy for C, while A and B are now joined by a new cross-tunnel allowing quicker resupply for brand new material... Again, much fun.)
I don't think marking stone for Dumping creates the same sort of "lost or misplaced" message for the earmarking construction or other use as it would if it was undermined by channelling or similar in-between assignment and a representative of Dwarfkind grabbing hold of the designated item, BICBW.