As a Wild Mass Guessing subpage, all spoilers are unmarked as per policy. You Have Been Warned.
Javier Hidalgo was possibly high
Consider the fact that during the final boss battle, Javier is laughing madly and talking of possibly "absorbing" poor Manuela into him so they can be together forever, only to suddenly ask Leon/Krauser to kill him at the end of the battle. He was on drugs up til that point, wherein the relapse occured and he wanted to die now that the high wore off.- It is really a bad sign when that makes sense.
Chris, Claire, and Krauser are all infected with the t-Veronica virus.
The games state that the t-Veronica virus is highly infectious. Yet these three should be infected. (Hell, maybe even Leon should be, too.) To elaborate, Chris and Claire (and Wesker) had to deal with Alexia flinging her infected blood, yet they do not end up infected. (Maybe the combusting-on-contact-with-air kills the virus?) Claire could have possibly been poisoned by Nosferatu. Steve was also a bloody mess when he died. If Claire so much as had a papercut... Javier ends up releasing spores, which infect the surrounding environment. Krauser has a Canon open wound. You do the math.- Plot Armor?
- It's pretty obvious that Krauser is infected with something (the mutant razor-arm is a dead giveaway). As for why the other characters never succumb to infection, it's possible Umbrella's viruses aren't nearly as infectious as we've been led to believe. Maybe it doesn't take just one scratch or one bite to get infected. Maybe you need a much bigger dose (i.e. several scratches/bites) for infection to take hold. Alternatively, maybe a person whose immune system is strong enough can fight off the virus naturally and the people/animals who succumb had weaker immune systems. Either or both of these theories could explain why the main characters don't get zombified. (And as a bonus, they would also explain why you can still find random uninfected survivors scattered throughout Raccoon City long after the initial infection takes hold.)
- Don't think Krauser is infected with it. Because in RE 4 the Plagas remover laser actually can affect him. Unless the T-Virus has traces of Las Plagas in them.
Leon is intentionally altering parts of the story for Krauser's sake
It would explain why, in the Resident Evil 2 segment the idea of him and Claire willingly splitting up (like what happened in the original game) is brought up and rejected at least twice. After all, it wouldn't instill confidence in your professional soldier comrade if you admitted that your zombie plan was developed by Leeroy Jenkins. Likewise, the Code: Veronica story is being told imperfectly on purpose
Keep two things in mind during the Code: Veronica segment. Firstly, Leon was never involved; all the knowledge he has on those events is what Claire would of told him. Secondly, the recollection happens after the second Operation: Javier mission, either whilst Leon is near-drowning in the river or is regaining consciousness afterwards. The former alone would mean Leon doesn't necessarily know everything that actually happened, but the second guarantees those recollections are going to be fairly shaky. Wesker sold Javier the T-Veronica to get a more viable sample.
Wesker got the his samples of Veronica from Steve's corpse, but being that he was mutated without the prerequisite 15 year cryo/organ transplants, he wasn't bonded with the virus like Alexia was, so the samples wesker obtained were unstable or incomplete, he needed a healthy host who had bonded with the virus to get a "perfect" sample of Veronica from, so he sold Veronica to Javier, knowing Javier wanted to save his daughters life, and would follow Weskers instructions to the letter, after Manuela became fully bonded with Veronica, and her life was saved, he knew Javier would probably not be adverse to giving Wesker a sample of her blood out of gratitude, and if he didn't Wesker could easily take it by force if need be.