Basically, when they're meeting in the treasury room, Ray's and Juarez dialogue lines are suggesting like they're meeting for the first time, they don't even know identity of each other... Which is completely not true, because both Ray and Thomas were working for Juan Mendosa in the past (and later they turned against him).

I know that making prequel (in this case - game Bound in Blood) in later term is always making such risks (discrepancies in the plot), but this one seems to be very obvious and hard to miss.

Well, for one thing, it was next to 20 years since they last met
and second, with all the shooting going on and how they only saw each other at a distance, it was probably difficult to see each other very clearly.
Also, Ray probably didn't know much to tell the difference between different Mexicans. Kinda like you meet Jackie Chan in a Chinese diner, then 20 years later you see him again but there's a dozen other Chinese people shooting and throwing chopsticks at you