You seem to have been facing the Cybran race, essentially cyborgs that have a penchant for spider-like mechs, as demonstrated by the Monkeylord you evidently faced.
It's worth noting that Mass Fabricators are pretty borked in most of the beta version out there, and you'll get most of your income from your Mass Extractors when you upgrade them. You should still build Mass Fabricators, but build them en-masse and directly adjacent to an energy generator, for reasons i'll explain below.
Now, whenever you build a factory, it's always a good idea to build a few energy generators directly adjacent to it, as it gives you a small [but noticable] production boost. Moreover, if you build mass storage tanks next to your Mass Extractors, you get a small mass production boost, which works the same way with Energy Generators and energy storage tanks.
All of this is explained rather deftly in the tutorial videos available on FilePlanet, here