This actually happened to me with a basic steam-style warmer and it drove me nuts during 2 a.m. feeds. I tried lowering the water level and cutting the timer by a minute, and descaling, which helped a little but the temp still jumped around depending on bottle size and starting temp.
What finally fixed it was switching to Philips Avent bottle warmer because it uses smart temperature control and a gentle water bath, so it stopped overshooting and gave me the same warm temp every time. It actually is a touch slower than the super fast steam ones, but the consistency and peace of mind were worth it.
If you keep your current warmer, try starting with room temp water, stop the cycle a bit early and swirl, and descale often. A quick check with a kitchen thermometer helped me learn how much to under-time it for different bottles.
