I suspect it could be a matter using "what's to hand" (as might be the case in an emergency), or worries about fumes if acetate catches fire or reacts to something else.
I'm hazarding a guess that in a sub if they've got the choice between two materials that have similar properties for the job they want, they'll go for the one that has less potential hazards, especially when it comes to smoke/fumes.
It's also possible the tracing paper is/was used for something else on board (engineering, plotting targets?), in which case it makes sense given a choice to take a larger supply of something with multiple uses, than two supplies that have one use.
Reading the article the tracing paper itself wasn't at fault, but rather the amount of stuff on it (notes, post it notes etc), which would cause problems regardless of what was used.
Anyway it's better that they make the mistake and put the ship out of action on a training exercise than in actual combat (and i'm betting they couldn't get the same real feeling in any simulator).