dammets89: I don't know, the way you describe it, you either triggered an alarm, encountered a rare bug in the game, or are greatly exaggeratting.
SlenderSilence: Pretty much. Enemies DO respawn, but only 1-3 at a time, and generally well away from the player, and even then, respawns don't start until later in the game . At the point in the game which the OP describes, there should only be two wrench hybrids in the immediate vicinity, and maybe 5 or 6 total in the accessible part of that map. Unless he triggered an alarm, or encountered some heretofore unheard of bug, there simply won't be 15 hybrids to fight.
Personally, I always thought SS2 handled respawning VERY well. Except when an alarm is triggered, you never face an endless stream of respawning enemies, a la Call of Duty, and the respawns that do occur, occur sparingly, . you never quite know if an area is completely safe, but generally once you've "cleared" a level, then the major threats are gone. In other words, it keeps you on your toes, without making you feel as if killing your enemies is futile.
THIS.
The only bad respawn area I have found, and I am at deck 4, is Cargo bay area in deck 1.