Not everyone gets hypercalcemia from Vit D ointments/supplements. It is a potential, but not that common.

Kidney stones (most of them anyway) are formed from high oxalate in the diet. --this is for calcium oxalate stones.

There are also uric acid stones.

pH of the urine may cause them -- citrate supplements are used
sometimes for calcium oxalate stones.

For the calcium oxalate ones, giving calcium citrate may prevent them. Eating a low oxalate diet too. It is believed that the excess oxalate may come from foods eaten, when the beneficial organism Oxalobacter formigenes dies from antibiotic use. Also vitamin B6 for some reason helps kidney stone prone patients prevent them. (for some odd reason).

There are some kidney stones that have bacteria as centers, and it is thought that they begin the process for some people.

The old belief that high calcium causes stones, is just not the total reasons for them. Calcium can be lost thru the urine commonly. The common diuretic furosemide (Lasix) causes a loss of calcium thru the urine.