This thread is surly a re-hash but can still be somewhat fun for new and returning players. Not really intended to be bug hunting and obsoleted due to past efforts or hard counts already known within the community.
My count is limited so far because it's based on recent actual play. Noticing these is kind of tricky IMO. Cutscene and plot is often spread out and sort of sparse, and some I just want to skip! ..also hearing the 'normal' words instead of the fictional may just not register as odd at first exposure.
The mistake I've kicked the thread off with became clear while I was trying different things -- mission repeated 2-3 times.
I'd guess the possibillity in finding these in plot and cutscenes is better. but perhaps there are some generic continuity breaks also.
NOTE: I'm not considering pronunciation differences in my list. In X3R alone I think there must be 6 or more variations of "Kha'ak"
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XBTF: n/a
XT: n/a
X2: 1 confirmed (1.5 english)
X3AP: n/a
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n/a = can't confirm or point out instance at this time