"Imagine someone at your work insisting that Java and Javascript are the same language."

This is a rather poor analogy. Someone confusing Java and Javascript might believe they can paste their Javascript code into a Java program and have it work. Nothing of this nature will result from confusing clips and magazines. A shooter isn't going to expect to be able to use their Mosin-Nagant clips with their PSL, any more than they would expect for the PSL magazines to be valid replacements for their Winchester 1895 magazines.

It is incorrect, but it's not all that bad. 95% of the time, it is clear from context; the remaining cases primarily concern weapons with a fixed magazine, for which the user probably does know the difference.

No true Scotsman... Really - this is a matter of taste (what slang you prefer). As a former arms dealer / in a family of government weapons contractors and servicemen, we all use "clip" as slang.

It's like everyone calling car wheels "rims"

Really? I am in the Canadian Forces infantry, and if anyone ever used the term "clip" in reference to a magazine, and was actually serious, I'm pretty sure they would get beat up. May I ask what country you are affiliated with and in what branch of the military those servicemen are? It is interesting to see such a basic difference in terminology.

USAF and small weapons / ammo manufactures. You're right - military nomenclature (US) uses very precise (and verbose) terminology: "magazine" is always used strictly. Though the words "gun" and "rifle" are dropped in favor of "weapon" in some cases. What I find is that the longer you're out, the more the language becomes civilian - unless you're a hardcore / die-hard kind of person.