i figured out the reason, one of the prestige upgrades are creating positive feetback loop, the one that gives you additional XP from your highest XP from a click, with big enough multiplier, grows becomes so rapid, that it overflows into inf in a matter of a couple dozens of clicks
I tested it again. As you said, if I dump some points to Increased and More upgrades after level 100, the game seems to enter a positive loop state. Hits 3000 level so easily.
This is not a problem under the 100 level, but I may fix the highest XP reward if I get more feedback.