The highest, by far, death numbers come from Mariupol. It's a city close to the Russian border that was attacked very early in the war, but didn't surrender quickly like most other cities in the South. The estimates are somewhere close to 25K dead in this city alone. Civilians were unable to evacuate, and it was the time when Russia had plenty of resources, especially artillery munitions to expend and their tactics were to do massive artillery bombardment (often with rocket artillery) before massive motorized assault. So, lack of precision, or as some jokingly call it "accuracy through saturation".

Since Mariupol fell to Russia, they never counted the dead. There are horror stories of the bodies not being buried for month after surrender, and in some cases, Russians simply pawed over the places with many dead (a prominent example is the theater in the city center, but there were more).

The numbers you are quoting are the "counted" ones. Mariupol, Sieverodonetsk, Kherson, saw a lot of deaths that were never counted.

Sorry to bring another conflict into the picture, but it's useful to illustrate the point. In Gaza, the "health ministry" used a different "technique" to count the dead. Normally, to establish that someone died, there has to be a qualified medical professional at the scene, they also have to get a hold of identifying documents (or else, they will be counted as "John/Jane Doe", but in the morgue, much later). In some "special" cases a non-medical professional may record a death (they are usually defined using the language like "the head is more than 50 cm away from the rest of the body" etc.) But they switched to "incorporating reports from the news sources" (i.e. if some newspaper reported X people killed in some event, they just added X to the tally).

After the front line stabilized in Ukraine, they had no reason (or excuse) to count their civilian casualties in the way Gaza administration did, so, they never incorporated those who were never properly reported. And that's why we have a relatively "low" numbers. If Ukraine is ever able to regain control of the territory captured after 2022, these numbers are bound to go much, much higher, as they will have to deal with eg. property ownership and would have to either declare the previous owners as deceased, or actually find them.