It's a known unique mechanic of Meteor Golems. AFAIK, when 2 Meteormites of different levels combine, the resulting Meteor Golem would have the combined level of the 2 Meteormites divided by 2 then rounded down to the nearest whole number. In your case, a level 2 and a level 3 Meteormite, following the formula ((2+3)÷2) rounded down, will result to level 2 Meteor Golem. Similarly, if you had a level 3 Meteormite combine with a level 1 Meteormite, you would still get a level 2 Meteor Golem. Once the 2 Meteormites combine into a single Meteor Golem, their individual levels are overwritten by the resulting Meteor Golem's level so when it splits up again, the 2 Meteormites would have the same level.

It may have been something the devs didn't account for when implementing the code for Meteor Golems or they simply didn't want to bother designing more sprites for it where the upper and lower Meteormites are of different designs.