the tip screen talks about robotbrains being a creation from general atomics international and isabel cruz says about coming to the commonwealth because the general atomic fabric and found the secret military base...

so why are the robotbrains and everything related to it in RobCo building? even the mechanist's lair is there

is this a huge mistake made during the writing?

RobCo and General Atomics having a joint contract with the U.S. government isn't really that hard to understand. Hell, Liberty Prime was made by both RobCo, General Atomics and the U.S. Military.

yeah, i knew about liberty prime, but for me, it was just because a special case

New Vegas had a Mr Handy in a RobCo owned facility, listed as a RobCo product, when all previous lore had only stated they were products of General Atomics.

From what we can gather, RobCo and General Atomics had a history of working together on robots.

Judging by the terminals it was seemlying another Joint project but was quickly taken over by the military who fired/killed or shipped to dead end posts anyone who disagreed...

Although apart from being the front company (and perhaps making the robot bodies) it doesn't seem like Robco had much involvement in the project, seeing as how they were experimenting on humans (be it convicts) this was probably done on purpose so anyone investigating the robobrains wouldn't think to look there.

Personally, I think the Mr. Handy at REPCONN was a mistake by Obsidian. As you said previous lore said that it was just GAI who made them. Fallout 3 says that Liberty Prime is the first joint project between RobCo and General Atomics, and in 4 Codsworth takes great pride in being a General Atomics product and if you take him to the Noodles Protectron he will suggest RobCo products are inferior to General Atomics. And the evidence most pointing towards it being a mistake is that Mister Handy was first brought to market in 2037, while RobCo wasn't founded till 2042, according to the wiki.