Yes. It's not "manufacturing software" (if I'm right about it being the factory control system), it's more like glue code tying all of the different bits and bobs of the assembly line together. This kind of system is usually built in ladder logic or function block diagrams rather than as source code, is typically a whole lot of very simple bits side by side, and often needs to be tweaked in realtime during production. It's likely that quite a few people (definitely more than 2-3) have direct access to modify this sort of code and are probably monitoring and fine tuning it continually.

It's not really comparable to your work where you're writing the OS or system code for a safety PLC or something, and you quite rightly have to maintain a very strict process where everything is fully documented and triple-checked so you can prove that it meets your target performance level. All of the stuff that does need that kind of precision is locked away into modules (like the aforementioned safety PLC) which just gets plugged together like Lego by most of the controls team.

(All this is kind of moot, though, because it says that the culprit used a few different logins to make their mischief. Depending on the permissions set for those logins they could have bypassed pretty much any formal workflow, at least temporarily.)