[PeterisP]

It kind of implies that - "AI Cheats at Old Atari Games by Finding Unknown Bugs" would be an accurate title, but the extended "AI Cheats at Old Atari Games by Finding Unknown Bugs in the Code" tells that it's actually finding something in the code, as opposed to simply unexpected/emergent behavior.

[pvg]

It's mildly ambiguous (like most things) but it's not misleading or inaccurate. It finds bugs. Which are in the code. It doesn't say what kind of code and it certainly doesn't say it finds them by looking at the source code.

[corobo]

I read it and presume it's meant to be read as the AI finding "unknown [bugs in the code]" as opposed to "unknown [bugs] in the code"