The prefix system uses phrases. Have you translated these yourself in the Admin CP? I hadn't mentioned it up to now as I assumed you would have known.
Really, there's a logical explanation for this so it's either being automatically translated, you're getting confused about which language you're using or you have translated the phrases yourself and forgotten.
Probably worth a follow up in case anyone runs into something similar.
When you create a prefix, the title you enter is converted into a phrase. For example, the first thread prefix will have a name of thread_prefix_1. The second one you create will have a name of thread_prefix_2 etc.
You can then translate these phrases in each language.
Phrases aren't automatically deleted when the prefixes are deleted so this is something to bear in mind.
To find all prefixes that have been translated; search each language for phrases with titles containing thread_prefix_ and delete them as necessary.