I think it depends on what you mean by a "medieval village" both in historical time and in physical size.
Cutting and shaping stone takes a lot of effort and skill, it is also expensive. Flagstones and setts differ. Flagstones take a lot more work and skill to provide flat relatively thin slabs... but even setts - which are smaller and more irregular take a certain amount of work.
Such materials get used for critical building components and cheaper materials used where expense is not necessary.
In posh houses you might find flags used inside buildings but you'd often only find compacted earth floor - depending on what historical era and region you are looking for.
You might find important roads had setts, cobbles or other metalled road surface, but the average track or rural lane could also simply be compacted dirt.
It would be highly unlikely to have a village 'paved' in flag stones - if you really want to use them then keep them for the posh areas (around important buildings - church grounds etc), the remainder at best would be setts/cobbles. But around the lesser buildings such as homes for the general populace i'd go for plain old dirt.
