As it was explained to me, it was territory marking/office politics. Editors back then were very powerful when it came to decisions on content. They did not take kindly to anyone explaining/telling them they had no control over any portion of the content.

> What did they think the code meant?

This gets interesting. They were told it was for the computers, but upon seeing high level language artifacts that looked vaguely like English words, they grabbed their red marking pens and leapt into action, absolutely certain they were in the right as they had always been in the past. This was at the very beginning. Later, it got more nuanced.

> What changes did they make, anyway?

Early incidents had stories of galleys using non-proportional font forced to change to proportional font simply due to aesthetics. Red pens changing the contents of PRINT statements (because it said "print", and that was their domain, right?). Even later with more lessons learned and nuances started to creep in, this was way before programmer fonts made the scene, and the typical goofs one would expect from manual transcription were rampant. The pipelines did not exist yet back then for a long time to take raw source code and dump them into the non-digital typesetting systems at the time, so it was all laboriously transcribed from printouts by non-technical staff.

> Did they learn to not touch math equations before?

Very little cross-pollination of editors experienced with math-heavy technical writing, and those overseeing print products popularizing BASIC programming. BYTE magazine was revolutionary at the time for realizing this, and even they had some gaffs from time to time.