When HEPHAESTUS was initially released into the printing matrix, Aloy and her team were much further away from HEPHAESTUS' machines than the massive group of Specters charging right at them, which would definitely be their focus at the time.
Later on, when the Zeniths' shields have been disabled, that appears to be when the battle between the Specters and HEPHAESTUS' machines spills over them, leading to them getting attacked by HEPHAESTUS' machines. Meanwhile, Aloy is rushing past the battle as quickly as she can (it's probably easier to avoid the attention of the the massive Slaughterspines and Dreadwings) while her teammates deal with the more eye-level Specters. However, it is interesting that Erend later states that they're dealing with the last few Specters, with no mention of HEPHAESTUS' machines.
Perhaps it was intended that HEPHAESTUS' machines were wiped out after the printing matrix self-destructed, leaving a manageable amount of Specters for Erend and the other to finish it? Perhaps HEPHAESTUS prioritized the Zeniths and Specters as it saw them as a greater threat? Perhaps with the amount of HEPHAESTUS code GAIA had obtained, she was able to influence the machines just enough to not attack the team at that moment? You do make an interesting point.
