When the surface water temperature is still well below the water boiling temperature, some bubbles at the bottom tend to float up but somehow the bubbles seem to disappear before reaching the surface. What is the most likely scenario for these bubbles?

The reasons why the seemingly floating bubbles disappear was that they tend to loss their latent heat to the water molecules at the surface water.

Explanation:

Heat energy has a considerable effect on the velocity of molecules including water. The water molecules below the container will receive much more heat energy than those above it. This heat energy in the form of specific heat capacity and latent heat that result in the increase in the speed of individual molecules of water and finally to the escape of the molecules to a colder region of the container, in this case the upper region. At the collision of the bottom water to the surface water, they tend to exchange their heat content, the hotter molecules will lose their heat to the cold ones. When the formerly hot molecules encounter this, it will result in lowering the temperature and consequentially to the reduction of their movement, once in the form of bubble, now become ordinary water. This convectional transfer of heat energy will continue until the whole system has a uniform temperature depending on the consistency of the heat source.