Why are these characters not "Mary Sues"? What were their weaknesses?

>Xenomorph in Alien:
unstoppable killing machine, incredibly tough, fast, smart.

>Xenomorph in Aliens:
pew pew - two bullets its dead.

They just had a flamethrower in Alien, right?

their weaknesses were that they had soul

not that asshat but they also had hilariously ineffective cattleprods

all those "elite" commandos were acting like pussy retards the entire time