Something that I have seem some times, not that frequent, but it does happened from time to time, is that you will see in level 1 bases, at the start of the game or even in some waves of level 1 enemies, one zealot that is level 15 and takes forever to dies as it has a ton of def/hp.

Is this intentional? I think it is quite weird, specially as for now I only have seem this with Zealots, not happened with any other race

Nope. It's a known issue by the unit level processor.

I'll bring back the "nuke biter" button as failsafe in next ERM release, which it'll kill any unit within 32 tile radius.